Failed species,innominate forms,and the vain search for species limits: cryptic diversity in dusky salamanders (Desmognathus) of eastern Tennessee

Cytochrome B sequences and allozymes reveal complex patterns of molecular variation in dusky salamander (Desmognathus) populations in eastern Tennessee. One group of allozymically distinctive populations, which we refer to as the Sinking Creek form (SCF), combines morphological attributes of Desmognathus fuscus with cytB sequences characteristic of Desmognathus carolinensis. This form is abruptly replaced by D. fuscus just north of Johnson City, TN with no evidence of either sympatry or gene exchange. To the south, allozymic markers indicate a broad zone of admixture with populations characterized by distinct cytB sequences and that may or may not be ultimately referable to Desmognathus conanti. A third distinctive group of populations, which we refer to as the Lemon Gap form (LGF), occurs in the foothills of the Great Smoky and southern Bald Mountains and exchanges genes with Desmognathus santeetlah along the escarpment of the Great Smokies, D. carolinensis in the southern Bald Mountains, and populations of a different haplotype clade in the Ridge and Valley. We treat all these as innominate forms that may represent “failed species,” recognizing that it may never be possible to reconcile species limits with patterns of phylogeny, morphology, and gene exchange in these salamanders.     

Control of spoilage fungi by lactic acid bacteria

The evaluation of the potentiality of lactic acid bacteria (LAB) strains isolated from different origins to inhibit mould growth and to identify and characterize the antifungal metabolites were the aims of this study. From a total of ninety-one LAB strains tested, ten were selected due to their high inhibitory effect (>80%). The antifungal activity of the majority of the selected LAB strains was lost after the neutralization treatment determining the acidic nature of the antifungal metabolites. Lactic, acetic and phenyllactic (PLA) acids were identified as being responsible for antifungal effect in the 10 cell-free supernatants (CFS) evaluated. Amongst the strains evaluated, only Lactobacillus fermentum CRL 251 produced fungus inhibitory peptide/s, smaller than 10 kDa, thermostable, active in the pH range of 4–7 and sensitive to trypsin. This is the first report on antifungal peptide/s produced by a L. fermentum strain.     

Identification of potential sources of airborne Olea pollen in the Southwest Iberian Peninsula

This study aims to determine the potential origin of Olea pollen recorded in Badajoz in the Southwest of the Iberian Peninsula during 2009–2011. This was achieved using a combination of daily average and diurnal (hourly) airborne Olea pollen counts recorded at Badajoz (south-western Spain) and Évora (south-eastern Portugal), an inventory of olive groves in the studied area and air mass trajectory calculations computed using the HYSPLIT model. Examining olive pollen episodes at Badajoz that had distinctly different diurnal cycles in olive pollen in relation to the mean, allowed us to identify three different scenarios where olive pollen can be transported to the city from either distant or nearby sources during conditions with slow air mass movements. Back trajectory analysis showed that olive pollen can be transported to Badajoz from the West on prevailing winds, either directly or on slow moving air masses, and from high densities of olive groves situated to the Southeast (e.g. Andalucía). Regional scale transport of olive pollen can result in increased nighttime concentrations of this important aeroallergen. This could be particularly important in Mediterranean countries where people can be outdoors during this time due to climate and lifestyle. Such studies that examine sources and the atmospheric transport of pollen are valuable for allergy sufferers and health care professionals because the information can be incorporated into forecasts, the outputs of which are used for avoiding exposure to aeroallergens and planning medication. The results of studies of this nature can also be used for examining gene flow in this important agricultural crop.     

Iron trafficking inside the brain

Iron, an essential element for all cells of the body, including those of the brain, is transported bound to transferrin in the blood and the general extracellular fluid of the body. The demonstration of transferrin receptors on brain capillary endothelial cells (BCECs) more than 20 years ago provided the evidence for the now accepted view that the first step in blood to brain transport of iron is receptor-mediated endocytosis of transferrin. Subsequent steps are less clear. However, recent investigations which form the basis of this review have shed some light on them and also indicate possible fruitful avenues for future research. They provide new evidence on how iron is released from transferrin on the abluminal surface of BCECs, including the role of astrocytes in this process, how iron is transported in brain extracellular fluid, and how iron is taken up by neurons and glial cells. We propose that the divalent metal transporter 1 is not involved in iron transport through the BCECs. Instead, iron is probably released from transferrin on the abluminal surface of these cells by the action of citrate and ATP that are released by astrocytes, which form a very close relationship with BCECs. Complexes of iron with citrate and ATP can then circulate in brain extracellular fluid and may be taken up in these low-molecular weight forms by all types of brain cells or be bound by transferrin and taken up by cells which express transferrin receptors. Some iron most likely also circulates bound to transferrin, as neurons contain both transferrin receptors and divalent metal transporter 1 and can take up transferrin-bound iron. The most likely source for transferrin in the brain interstitium derives from diffusion from the ventricles. Neurons express the iron exporting carrier, ferroportin, which probably allows them to excrete unneeded iron. Astrocytes lack transferrin receptors. Their source of iron is probably that released from transferrin on the abluminal surface of BCECs. They probably to export iron by a mechanism involving a membrane-bound form of the ferroxidase, ceruloplasmin. Oligodendrocytes also lack transferrin receptors. They probably take up non-transferrin bound iron that gets incorporated in newly synthesized transferrin, which may play an important role for intracellular iron transport.     

Molecular engineering as an approach to design new functional properties of alginate

Through enzymatic modification, we are now able to manipulate the composition and sequential nanostructures of alginate, one of the most versatile gelling polymers found in nature. Here we report the application of a set of processive polymer-modifying epimerases for the preparation of novel alginates with highly improved functional properties essential for numerous applications as gel matrices. Gels of enzymatically engineered alginate were found to be more elastic and compact, less permeable, and extremely stable under physiological conditions, offering significant advantages over native alginates. As a result, this study shows that, by controlling alginate nanostructure, its macroscopic properties can be highly controlled. The ability to tailor alginate has a great impact on the wide use of this biomaterial in industry and medicine. More importantly, this adds more knowledge to the link between polymer nanostructure and macroscopic properties and may serve as a model system for other polymer-based materials.     

Identifying novel sequence variants of RNA 3D motifs

Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are constructed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions generated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas handle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Validation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to automatically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download.     

Postural changes after sustained neck muscle contraction in persons with a lower leg amputation

Lower leg amputation generally induces asymmetrical weight-bearing, even after rehabilitation treatment is completed. This is detrimental to the amputees’ long term quality of life. In particular, increasing strains on joint surfaces that receive additional weight load causes back and leg pain, premature wear and tear and arthritis. This pilot study was designed to determine whether subjects with lower leg amputation experience postural post-effects after muscle contraction, a phenomenon already observed in healthy subjects, and whether this could improve the weight-bearing on their prosthesis.Fifteen subjects with a unilateral lower leg amputation and 17 control subjects volunteered to participate in this study. Centre of pressure (CP) position was recorded during standing posture, under eyes closed and open conditions. Recordings were carried out before the subjects performed a 30-s voluntary isometric lateral neck muscle contraction, and again 1 and 4 min after the contraction.Postural post-effects characterized by CP shift, occurred in the medio-lateral plane in the majority of the amputated (7/15 eyes closed, 9/15 eyes open) and control (9/17 eyes closed, 11/17 eyes open) subjects after the contraction. Half of these subjects had a CP shift towards the side of the contraction and the other half towards the opposite side. In four amputated subjects tested 3 months apart, shift direction remained constant. These postural changes occurred without increase in CP velocity.Thus, a 30-s voluntary isometric contraction can change the standing posture of persons with lower leg amputation. The post-effects might result from the adaptation of the postural frame of reference to the proprioceptive messages associated with the isometric contraction.