Molecular Diagnostics — an upper division/graduate course

We have developed a course in Molecular Diagnostics suitable as an upper division/Master’s level elective class for Biology, Microbiology, and Biochemistry majors who have already been introduced to basic genetics and molecular biology. The course provides an intensive hands-on laboratory experience in current molecular techniques for disease diagnosis coupled with lecture on major biological topics and concepts underlying disease and disease processes. Its structure and content make the course appropriate not only for students who envision careers in molecular diagnosis, but also for those aspiring to the teaching, research, or medical professions.     

Aneuploidy in upper gastro-intestinal tract cancers--a potential prognostic marker?

Chromosomal instability manifesting as aneuploidy is the most frequently observed abnormality in solid tumours. However, the role of aneuploidy as a cause or consequence of cancer remains a controversial topic. In this review, we focus on the karyotypic imbalances recorded for cancers of the upper gastro-intestinal (GI) tract, together with their associated pre-malignant lesions and the potential of aneuploidy as a clinical tool for patient management. Numeric chromosomal aberrations are common throughout gastro-oesophageal cancers and their precursor lesions. Additionally, specific chromosomal aneusomies have been identified as early changes in pre-dysplastic tissues suggesting they may be actively involved in driving tumourigenesis. As a progressive increase in the severity of aneuploidy with neoplastic progression has also been observed, it has thus been shown to be a useful prognostic indicator for patient classification as low or high-risk cases for cancer development. However, the biological basis for the aneuploidy in cancers of the upper GI tract needs to be established to understand its consequences and role during carcinogenesis, which is necessary for improving diagnostics and establishing novel targeted therapies.     

The upper temperature of life--where do we draw the line?

A new archaeal isolate has been reported that is capable of growing at up to 121 degrees C. The hyperthermophile, dubbed strain 121, grows chemoautotrophically using formate as an electron donor and FeIII as an electron acceptor and is closely related to members of the archaeal genera Pyrodictium and Pyrobaculum. Although the reported maximum growth temperature of strain 121 is 8 degrees C higher than the previous record holder (Pyrolobus fumarii; Tmax = 113 degrees C), the two organisms have virtually the same optimal growth temperatures.     

Is there enhanced lymphatic function in upper body trained females?

BACKGROUND: Chronic physical activity results in adaptations in many aspects of human physiology, while specific training can directly influence structural changes. It remains unknown if habitual exercise influences upper extremity lymphatic function in females; thus, the purpose of this cross-sectional study was to compare different exercise stresses on lymphatic function in ten upper body trained females with ten untrained females. METHODS AND RESULTS: Participants underwent a maximal upper body aerobic test on an arm crank ergometer before undergoing three randomly assigned lymphatic stress tests. Lymphoscintigraphy was used to quantify lymphatic function. (99m)Tc-antimony colloid was injected into the third web space of each hand, followed by 1 min spot views taken with a gamma-radiation camera. The maximal stress test required individuals to repeat their initial maximal exercise test. The subjects were then imaged every 10 min until 60 min were reached. The submaximal stress test involved arm cranking for 2.5 min at 0.6 W x kg(-1), followed by 2.5 min of rest, repeated for 60 min. The final stress test was a 60 min seated resting session. The clearance rate (CR) and axillary uptake (AX) were determined. Only AX post maximal exercise was significantly different between trained and untrained, p=0.009. All other measures of lymphatic function between groups were similar. CONCLUSION: This study demonstrates no significant difference in lymphatic function between upper body trained and untrained females.     

Brushing cytology of the upper gastrointestinal tract. Obsolete or not?

The merit of brushing cytology of the upper gastrointestinal tract has been questioned since it appears to duplicate biopsy. To determine its value, the reports on all endoscopic biopsy and cytology specimens from a one-year period were reviewed. The 683 procedures included 481 in which only a histologic biopsy sample was obtained, 47 in which only a cytologic brushing sample was obtained and 155 in which both types of samples were obtained ("combined specimens"). Among the 155 combined specimens, 4 of the confirmed malignancies were detected by histology only while 2 were detected by cytology only. A diagnosis of suspicious or positive for malignancy was made for 20% of the combined specimens as compared to less than 5% of the biopsy-only or brushing-only specimens. While 15% of the specimens that included a brushing sample (either alone or with biopsy) showed fungal infections, only 1.2% of the biopsy-only specimens did. It appears that the clinicians at this hospital tend to use brushing in combination with biopsy when either a malignancy or a fungal infection is suspected. Other empiric advantages of endoscopic brushing cytology include its rapid turn-around time, minimal invasiveness and good recognition of lymphoid cells. The selective use of brushing cytology should increase the probability of detecting malignancies and fungal infections without any increased risk or discomfort to the patients.     

MR microscopy of the human fetal upper extremity – a proof-of-principle study

Background

Bone morphogenetic proteins regulate multiple processes in embryonic development, including early dorso-ventral patterning and neural crest development. BMPs activate heteromeric receptor complexes consisting of type I and type II receptor-serine/threonine kinases. BMP receptors Ia and Ib, also known as ALK3 and ALK6 respectively, are the most common type I receptors that likely mediate most BMP signaling events. Since early expression patterns and functions in Xenopus laevis development have not been described, we have addressed these questions in the present study.

Results

Here we have analyzed the temporal and spatial expression patterns of ALK3 and ALK6; we have also carried out loss-of-function studies to define the function of these receptors in early Xenopus development. We detected both redundant and non-redundant roles of ALK3 and ALK6 in dorso-ventral patterning. From late gastrula stages onwards, their expression patterns diverged, which correlated with a specific, non-redundant requirement of ALK6 in post-gastrula neural crest cells. ALK6 was essential for induction of neural crest cell fate and further development of the neural crest and its derivatives.

Conclusions

ALK3 and ALK6 both contribute to the gene regulatory network that regulates dorso-ventral patterning; they play partially overlapping and partially non-redundant roles in this process. ALK3 and ALK6 are independently required for the spatially restricted activation of BMP signaling and msx2 upregulation at the neural plate border, whereas in post-gastrula development ALK6 exerts a highly specific, conserved function in neural crest development.

     

The upper paleolithic burial area at Predmostí: ritual and taphonomy

Paleoanthropological materials from Predmostí, recovered by J. Wankel in 1884, K.J. Maska in 1894, M. Kríz in 1895, and K. Absolon in 1928 (and probably 1930), represent one of the largest collections of early modern human remains. Unfortunately, most of these fossils were destroyed in 1945. The aim of this paper is to create a list of finds in accordance with the discovery dates, to place them into the spatial and chronological context of the site, and to compare them with the evidence from recent excavation in 2006. Two competing hypotheses are raised in the literature suggesting that the Predmostí individuals represent either a contemporary burial as a consequence of one catastrophic event, or a gradual accumulation of human bodies at one place. Whereas the first hypothesis is supported by the demographic structure of the buried group, including adults and children, the second interpretation is based on stratigraphic and taphonomic analysis of the burial area itself. Using the original documentation of Maska and other early researchers, and my own experience from recent excavation in the remaining part of the site, I attempt to reconstruct the plan of the site, with a focus on spatial distribution of the human fossils, especially in the main burial area. I suggest that the burial place was not the settlement center, but rather a peripheral and task-specific area. The determining factor for location of the burial area was likely the remarkable Skalka rock, a cliff that rose directly above the site. A long-term tendency to place the dead "below the rock" may have given rise to the accumulation of human remains at a single place, with a scatter of dispersed fragments in the vicinity. At this location, the human bodies were partly protected by soil coverage, limestone debris, and mammoth scapulae, but were also affected by postdepositional processes such as redeposition of sediments, predator activities, and later human activities, including the burial of additional corpses.     

How close to a pendulum is human upper limb movement during walking?

The aim of this work was to investigate how close to pendulum-like behaviour the periodic motion of the human upper limb (or upper extremity) is, during normal walking at a comfortable speed of locomotion. Twenty-five healthy young persons (males and females) participated in the experiment. Biomechanical testing was undertaken (mass and centre of mass of each segment of the total upper extremity). Participants were walking on a treadmill with a standardised velocity of 1.1 ms(-1) (comfortable speed for all of them). A video analysis system with Silicon software was used to measure the different angles of the arm and forearm. The theoretical period of motion and maximal angular velocity were computed for the centre of mass of the total upper limb from the measured phases of the arm swing and associated positional potential energies. Actual measured periods of motion, in comparison, represented a level of similarity to a lightly damped simple pendulum. Using this assumption, the "damping factor" was calculated from the ratio between theoretical and measured values. A vast majority of people exhibited an actual angular velocity exceeding the expected theoretical angular velocity calculated for a virtual pendulum of similar mass and length characteristics. This may be due to muscle forces that are contributing to the motion of the upper limb during walking rather than simple gravity force acting alone. The observed positional potential energy of the dominant limb was greater than that of the non-dominant limb for the vast majority of participants.     

Vegetation types of the upper Madeira River in Rondônia,Brazil

We characterize the vegetation types of the upper basin of the Madeira River in the Brazilan state of Rondônia, a biodiverse region with elevated rates of habitat loss. Vegetation and environmental parameters were recorded from 37 observation points distributed along and near a 160 km stretch of the Madeira River and representing the range of regional environments. Analysis of structure and floristic variables, as well as associated edaphic attributes and water table fluctuation, permitted recognition of five main vegetation types and seven subtypes. Open Ombrophilous Forest was the most frequently encountered vegetation type and occurred on well-drained, nutrient-poor soils, whereas Dense Ombrophilous Forest was seldom recorded. Alluvial Ombrophilous Forests (várzea) were found along a narrow strip of land along the banks of the Madeira River on the most fertile soils in the study area. Semideciduous Forests were found on small areas of rocky outcrops with shallow soils and reduced water availability during the dry season. Campinaranas, which range from open savanna physiognomies to closed canopy forests, were found to be a key environment in the lowlands south of the Madeira River on silty hydromorphic soils, where they harbor a peculiar flora tolerant of flooding during the rainy season. Our classification of the main vegetation types in the upper Madeira River illuminates a high degree of floristic and environmental heterogeneity in a highly threatened region. Our results will be useful for designing conservation strategies aimed at protecting the full range of floristic diversity present in the region.     

A suggested relationship between sugar beet leaf spot and upper—air flow patterns

The flow pattern of the upper air at the 500 mb level was found to be the key to the surface weather pattern influencing the development of CERCOSPORA BETICOLA on sugar beet. Stable long-wave conditions of the upper air provided more persistent surface conditions unfavorable for leaf spot development. A train of short wave produced favorable weather conditions for leaf spot development.

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Zusammenfassung Es wurde nachgewiesen, dass die Strömungsformen der oberen Luftschichten auf dem 500 mb Niveau die Wetterformen an der Oberfläche beeinflussen, die die Entwicklung von CERCOSPORA BETICOLA auf Zuckerrüben erklären. Stabile Langwellen-Bedingungen in den oberen Luftschichten bedingen gleichmässigere Oberflächenbedingungen, die für die Blattflecken ungünstig sind, während eine Folge kurzer Wellen zu Wetterbedingungen führt, die für die Blattfleckenbildung günstig sind.

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Resume On a pu démontrer que la forme de l'écoulement de l'air au niveau de 500 mb se répercute sur les conditions atmosphériques au sol, conditions particulières qui agissent sur le développement de CERCOSPORA BETICOLA de la betterave à sucre. Des conditions stables d'écoulement ne présentant que de larges ondulations dans les couches supérieures de l'atmosphère provoquent des conditions de surface défavorables au développement de la maladie. Au contraire, une succession de courtes ondulations conduit à des conditions de surface favorables au champignon.

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Journal Paper No. J-6610 of the Iowa Agriculture and Home Economics Experiment Station, Project 1163. Cooperative investigation of the Iowa Station and Crops Research Division, Agricultural Research Division, United States Department of Agriculture.     

Training for voluntarily increasing individual upper α power as a method for cognitive enhancement

In order to estimate the effect of simultaneous α EEG stimulating and electromyogram (EMG) decreasing biofeedback training on the α activity and cognitive functions, fluency, accuracy, and flexibility during cognitive tasks, as well as α-activity characteristics before, during, and after ten training sessions of voluntarily increasing α power in an individual upper α range with the eyes closed were studied in 27 healthy men aged 18–34 years. To isolate the biofeedback effect in training for the α power increase, data on two groups of subjects were compared: an experimental group (14 subjects) with true biofeedback and a control group (13 subjects) with sham biofeedback. Follow-up testing was performed one month after the end of training to estimate the stability of the effect. The results showed that the training for the upper α power increase using biofeedback increased the frequency, width, and power in an individual upper α range at rest and improved cognitive performance only in subjects with a low baseline α frequency. Conversely, sham biofeedback training (without the feedback signal) increased the α power, though less efficiently, only in subjects with a high baseline α frequency, this increase was not accompanied by improved cognitive performance. The biofeedback α training eliminated the decrease in the α amplitude in response to a cognitive task after the biofeedback training course, this effect being preserved within one month. It may be concluded that α EEG-EMG biofeedback training can be used for improving cognitive processes in healthy subjects, as well as for prognostic purposes in clinical practice and in the brain-computer interface technology.     

Pollen-analytical reconstruction of vegetation in the upper regions of the Orlické hory mountains,Czechoslovakia

The paper presents the results of pollen analyses of samples collected from two peat localities in the Orlické hory mountains in Czechoslovakia. Appended pollen diagrams depict the vegetation and its changes in the Older and Younger Subatlantic period. The paper suggests the probable proportional representation of the principal woody plants in the area and, on the basis of pollen analyses, reconstructs the forest covers of the Orlické hory, especially of their upper regions. The author has foundFagus to have predominated among woody plants in the area (even in the upper regions) in the Older Subatlantic. From the 16th or 17th century onward it was gradually replaced byPicea. This change was primarily due to human activity (cutting down of the beeches). The composition of foot-hill forests, as far as it is reflected in the diagrams, is discussed. The pollen diagrams also testify to agricultural activity by man in the wide surroundings of the Orlické hory.     

Diversity and genetic distance in populations of Steindachnerina in the upper Paraná river floodplain of Brazil

Whereas four species of the genus Steindachnerina occur in the Paraná river basin, S. insculpta was the only endemic species of the region under analysis, which is the third lower section of the upper Paraná river. Among other factors, this species has been characterised by the absence of spots in the basal region of the dorsal fin. However, various specimens with this characteristic appeared in the region after the construction of the Itaipu Hydroelectric Plant in 1982. An analysis of the genetic variability of Steindachnerina populations with or without spots is provided. Specimens were collected in different sites of the floodplain of the upper Paraná river and samples were compared by random amplified polymorphic DNA (RAPD) technique and morphological analyses. Ninety-eight amplified loci with nine random primers were analysed in 19 specimens of each phenotype. Data for genetic distance showed great divergences between the two phenotypes and indicate two different species. Spotted specimens may be identified as S. brevipinna, found in the region downstream Sete Quedas Falls. The species must have overcome the geographical barrier during the building of the Itaipu hydroelectric dam that submerged the waterfalls and which became an obstacle between the upper and middle Paraná river some 150 km downstream. Since phenotypes do not share dominant alleles, absence of gene flow has been suggested.     

An 800 year record of mangrove dynamics and human activities in the upper Gulf of Thailand

A multiproxy record comprising pollen, charcoal, loss on ignition and particle size analyses from two radiocarbon dated sediment cores from Klong Kone subdistrict on the western coast of the Gulf of Thailand provides insights on mangrove dynamics, environmental changes and human activities during the last 800 years. The mangroves were dominated by Rhizophora which indicates that the area has been influenced by the sea level from at least 820 cal bp until 720 cal bp. An intertidal area may have formed that supported mangrove development as part of an old shoreline during 820–720 cal bp. After 720 cal bp, mangroves decreased and were replaced by grasses, suggesting that a lower sea level caused the mangroves to grow closer to the sea until around 140 cal bp. Cereal pollen increased from 720 cal bp suggesting probable use of the shoreline for intensive cultivation. The mangroves were characterised by Avicennia, which increased toward the top of the 2 cores, suggesting that the mangroves then grew further inland, probably due to recent sea-level rise. Intensive human activity is recorded during the 20th century, as indicated by increased particle size, charcoal and carbonate content. At present, human activity in the area includes dams and construction as well as aquaculture.     

Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

Human tracheobronchial epithelial cells grown in air-liquid interface culture have emerged as a powerful tool for the study of airway biology. In this study, we have investigated whether this culture system produces "mucus" with a protein composition similar to that of in vivo, induced airway secretions. Previous compositional studies of mucous secretions have greatly underrepresented the contribution of mucins, which are major structural components of normal mucus. To overcome this limitation, we have used a mass spectrometry-based approach centered on prior separation of the mucins from the majority of the other proteins. Using this approach, we have compared the protein composition of apical secretions (AS) from well-differentiated primary human tracheobronchial cells grown at air-liquid interface and human tracheobronchial normal induced sputum (IS). A total of 186 proteins were identified, 134 from AS and 136 from IS; 84 proteins were common to both secretions, with host defense proteins being predominant. The epithelial mucins MUC1, MUC4, and MUC16 and the gel-forming mucins MUC5B and MUC5AC were identified in both secretions. Refractometry showed that the gel-forming mucins were the major contributors by mass to both secretions. When the composition of the IS was corrected for proteins that were most likely derived from saliva, serum, and migratory cells, there was considerable similarity between the two secretions, in particular, in the category of host defense proteins, which includes the mucins. This shows that the primary cell culture system is an important model for study of aspects of innate defense of the upper airways related specifically to mucus consisting solely of airway cell products.