Voxel-based analysis in radiation oncology: A methodological cookbook

Recently, 2D or 3D methods for dose distribution analysis have been proposed as evolutions of the Dose Volume Histogram (DVH) approaches. Those methods, collectively referred to as pixel- or voxel-based (VB) methods, evaluate local dose response patterns and go beyond the organ-based philosophy of Normal Tissue Complication Probability (NTCP) modelling. VB methods have been introduced in the context of radiation oncology in the very last years following the virtuous example of neuroimaging experience. In radiation oncology setting, dose mapping is a suitable scheme to compare spatial patterns of local dose distributions between patients who develop toxicity and who do not.In this critical review, we present the methods that include spatial dose distribution information for evaluating different toxicity endpoints after radiation therapy. The review addresses two main topics. First, the critical aspects in dose map building, namely the spatial normalization of the dose distributions from different patients. Then, the issues related to the actual dose map comparison, i.e. the viable options for a robust VB statistical analysis and the potential pitfalls related to the adopted solutions. To elucidate the different theoretical and technical issues, the covered topics are illustrated in relation to practical applications found in the existing literature.We conclude the overview on the VB philosophy in radiation oncology by introducing new phenomenological approaches to NTCP modelling that accounts for inhomogeneous organ radiosensitivity.     

Functional analysis of phospholipase Dδ family in tobacco pollen tubes

Phosphatidic acid (PA), an important signalling and metabolic phospholipid, is predominantly localized in the subapical plasma membrane (PM) of growing pollen tubes. PA can be produced from structural phospholipids by phospholipase D (PLD), but the isoforms responsible for production of PM PA were not identified yet and their functional roles remain unknown. Following genome‐wide bioinformatic analysis of the PLD family in tobacco, we focused on the pollen‐overrepresented PLDδ class. Combining live‐cell imaging, gene overexpression, lipid‐binding and structural bioinformatics, we characterized five NtPLDδ isoforms. Distinct PLDδ isoforms preferentially localize to the cytoplasm or subapical PM. Using fluorescence recovery after photobleaching, domain deletion and swapping analyses we show that membrane‐bound PLDδs are tightly bound to PM, primarily via the central catalytic domain. Overexpression analyses suggested isoform PLDδ3 as the most important member of the PLDδ subfamily active in pollen tubes. Moreover, only PLDδ3 shows significant constitutive PLD activity in vivo and, in turn, PA promotes binding of PLDδ3 to the PM. This forms a positive feedback loop leading to PA accumulation and the formation of massive PM invaginations. Tightly controlled production of PA generated by PLDδ3 at the PM is important for maintaining the balance between various membrane trafficking processes that are crucial for plant cell tip growth.     

A dynamic culture platform enhances the efficiency of the 3D HUVEC-based tube formation assay

Cell-based in vitro biological models traditionally use monolayer cell cultures grown over plastic surfaces bathing in static media. Higher fidelity to a natural biological tissue is expected to result from growing the cells in a three-dimensional (3D) matrix. However, due to the decreased rate of diffusion inherent to increased distances within a tridimensional space, proper fluidic conditions are needed in this setting to better approximate a physiological environment. To this aim, we here propose a prototypal dynamic cell culture platform for the automatic medium replacement, via periodic perfusion flow, in a human umbilical vein endothelial cell (HUVECs) culture seeded in a Geltrex™ matrix. A state-of-the-art angiogenesis assay performed in these dynamic conditions showed sizable effects with respect to conventional static control cultures, with significantly enhanced pro-(dual antiplatelet therapy [DAPT]) and anti-(EDTA) angiogenic compound activity. In particular, dynamic culture conditions (a) enhance the 3D-organization of HUVECs into microtubule structure; (b) accelerate and improve endothelial tube formation by HUVECs in the presence of DAPT; (c) are able to completely revert the blocking effects of EDTA. These evidence emphasize the need of setting proper fluidic conditions for a better approximation of a physiological environment as an appropriate evolution of current cell culture paradigms.     

Sieve elements rapidly develop ‘nacreous walls’ following injury − a common wounding response?

Thick glistening cell walls occur in sieve tubes of all major land plant taxa. Historically, these ‘nacreous walls’ have been considered a diagnostic feature of sieve elements; they represent a conundrum, though, in the context of the widely accepted pressure–flow theory as they severely constrict sieve tubes. We employed the cucurbit Gerrardanthus macrorhizus as a model to study nacreous walls in sieve elements by standard and in situ confocal microscopy and electron microscopy, focusing on changes in functional sieve tubes that occur when prepared for microscopic observation. Over 90% of sieve elements in tissue sections processed for microscopy by standard methods exhibit nacreous walls. Sieve elements in whole, live plants that were actively transporting as shown by phloem‐mobile tracers, lacked nacreous walls and exhibited open lumina of circular cross‐sections instead, an appropriate structure for Münch‐type mass flow of the cell contents. Puncturing of transporting sieve elements with micropipettes triggered the rapid (<1 min) development of nacreous walls that occluded the cell lumen almost completely. We conclude that nacreous walls are preparation artefacts rather than structural features of transporting sieve elements. Nacreous walls in land plants resemble the reversibly swellable walls found in various algae, suggesting that they may function in turgor buffering, the amelioration of osmotic stress, wounding‐induced sieve tube occlusion, and possibly local defence responses of the phloem.     

Onset of feeding in juvenile sea urchins and its relation to nutrient signalling

The purple sea urchin, Strongylocentrotus purpuratus, has been the focus of extensive ecological and developmental research over the years. Strongylocentrotus purpuratus larvae transition into the juvenile stage after an extensive planktonic period. The metamorphic transition is characterized by dramatic changes in morphology and physiology of the juvenile compared to the larval form and mechanisms underlying this process, especially the early days post-settlement, remain poorly understood. We used SEM and phalloidin stain analysis as well as whole mount in situ hybridization to gain a detailed understanding of juvenile development in relation to nutrient signalling [insulin-like growth factor (IIS), FoxO (forkhead box, sub-group ‘O’) and TOR (target of rampamycin), also known as IIS/TOR/FoxO signalling]. Our results show that the majority of juvenile feeding features are fully developed only after 8-days of juvenile development, leaving an extensive period of nutritional stress. We found that FoxO gene expression increases during that time period and is localized in juvenile tube feet, potentially associated with sensory structures involved in nutrient signalling. Our data complement existing work on sea urchin juvenile development and shed new light on the perimetamorphic period of Strongylocentrotus purpuratus, with respect to nutrient signalling and the potential stressful pre-feeding period of juvenile sea urchins.     

Wnt‐3 and Wnt‐3a play different region‐specific roles in neural crest development in avians

Wnt signalling regulates cell proliferation and cell fate determination during embryogenesis. However, little is known about the developmental role of one Wnt family member, Wnt‐3, during avian development. To investigate the possible functions of Wnt‐3, its expression pattern was determined using whole‐mount in situ hybridization. Wnt‐3 is expressed in important signalling centres, including the dorsal neural tube, Hensen's node and the AER (apical ectodermal ridge). Most interestingly, Wnt‐3 is expressed in the dorsal neural tube as a gradient, with the strongest expression anterior in the trunk. Furthermore, this study showed that Wnt‐3 and Wnt‐3a play a different role in neural crest lineages derived from different axial level of neural tube. Wnt‐3 might be involved in proliferation of neural crest lineages, whereas Wnt‐3a plays an important role in melanogenesis in vagal. However, both Wnt‐3 and Wnt‐3a cause a significant increase in melanogenesis in the trunk neural crest lineage.     

Distribution of F-actin and Microtubules in Pollen and Pollen Tube of Lilium davidii

F-actin and microtubules are important components of pollen tube, which have very important function in cytoplasm streaming of pollen tube. The authors observed the distribution of Factin and microtubules in the pollen tube of Lilium davidii Duch. by immunofluorescence technique and confocol laser scanning microscopy, through which some new results were obtained. 1. Chemical fixation could preserve F-actin well in pollen tube, so the relation between F-actin and microtubules could be studied by the methods of chemical fixation and fluorescence labelling in pollen tube. 2. F-actin bundles were absent near the pollen tube tip, while microtubules were abundant and web formed in the pollen tube tip. The authors found that the terminal of microtubules was closely associated with the plasma membrane in the pollen tube tip. 3. Only a few F-actin bundles co-exist with the microtubules in the pollen tube of Lilium davidii. The results provided new evidence for the fimction and relationship between F-actin and microtubules in the pollen tube.     

Immunoblots of Integrin-like Proteins in Pollen Tube Membrane of Hemerocallis citrina

Antiserum against human VnR integrin, and ay, β3 integrin subunit cytoplasmic domain in Western blots were applied to determine if integrin-like proteins be present in the pollen tube membrane of Hemerocallis citrina Baroni. The results showed that anti-β3 integrin subunit serum could recognize 140 kD and 97 kD bands in SDS-PAGE gels under the reducing conditions, while antiserum against VnR and ay integrin could recognize 160 kD and 155 kD bands respectively under the reducing conditions, and also two small bands of higher molecular weight under the non-reducing conditions. Non-immune semm control could not cross react with any protein bands. The present study suggest that the integTin-like protein, the receptor of vitronecttn could exist in the form of av and β3 subunits in the pollen tube membrane, with its molecular mass quite similar to that of the integrin reported in animal.