Predicting the thermal distribution in a convective wavy fin using a novel training physics-informed neural network method

Fins are widely used in many industrial applications, including heat exchangers. They benefit from a relatively economical design cost, are lightweight, and are quite miniature. Thus, this study investigates the influence of a wavy fin structure subjected to convective effects with internal heat generation. The thermal distribution, considered a steady condition in one dimension, is described by a unique implementation of a physics-informed neural network (PINN) as part of machine-learning intelligent strategies for analyzing heat transfer in a convective wavy fin. This novel research explores the use of PINNs to examine the effect of the nonlinearity of temperature equation and boundary conditions by altering the hyperparameters of the architecture. The non-linear ordinary differential equation (ODE) involved with heat transfer is reduced into a dimensionless form utilizing the non-dimensional variables to simplify the problem. Furthermore, Runge-Kutta Fehlberg's fourth-fifth order (RKF-45) approach is implemented to evaluate the simplified equations numerically. To predict the wavy fin's heat transfer properties, an advanced neural network model is created without using a traditional data-driven approach, the ability to solve ODEs explicitly by incorporating a mean squared error-based loss function. The obtained results divulge that an increase in the thermal conductivity variable upsurges the thermal distribution. In contrast, a decrease in temperature profile is caused due to the augmentation in the convective-conductive variable values.

Sustainable freshwater production using novel cascade solar still with phase change material, serpentine water path, and copper fins

Heat losses in solar stills are high, which has led to a decrease in their thermal efficiency. Also, the production of these devices is limited to the presence of the sun, and their production stops during cloudy hours or at night. To solve these problems, in this experimental study, two cascade solar stills are examined under relatively similar conditions for sustainable freshwater production. One of these solar stills is modified with the phase change material and copper fins, and another one is a conventional cascade solar still without using the phase change material and copper fins. Paraffin was selected as a heat storage material to increase the time of desalination of water by the solar still. In addition, the copper fins are used to increase the conduction heat transfer in phase change material and provide better melting and solidification processes. To prolong the water path along the steps, the serpentine water path was considered. The results showed that at sunset hours, desalination efficiency with phase changing material and fins was increased. At 5 pm, the efficiency of the modified device was increased by 29% (on average) as compared to the conventional solar still without using phase changing material and fins. The rate of water production in conventional solar still in midday was higher compared to the modified solar still. However, in the sunset and night hours, the modified solar still has a higher production rate due to heat released from the thermal storage system.

Impaired fin regeneration and angiogenesis in aged zebrafish and turquoise killifish

Impaired wound healing is associated with aging and has significant effects on human health on an individual level, but also the whole health care sector. Deficient angiogenesis appears to be involved in the process, but the underlying biology is still poorly understood. This is at least partially being explained by complexity and costs in using mammalian aging models. To understand aging-related vascular biology of impaired wound healing, we have utilized zebrafish and turquoise killifish fin regeneration models. The regeneration of caudal fin after resection was significantly reduced in old individuals in both species. Age-related changes in angiogenesis, vascular density and expression levels of angiogenesis biomarker VEGF-A were observed. Furthermore, anti-angiogenic drug, vascular endothelial growth factor receptor blocking inhibitor SU5416 reduced regeneration indicating a key role for angiogenesis in the regeneration of aging caudal fin despite aging-related changes in vasculature. Taken together, our data indicates that these fish fin regeneration models are suitable for studying aging-related decline in wound healing and associated alterations in aging vasculature.

Application of heat sinks inside the pyramid solar distiller: experimental study on distiller performance under various operating conditions

Solar still is a cheap decentralized mode for obtaining potable water from saline water using solar energy, but it has low productivity. Previous studies showed that using pin fins in the absorber can increase the solar still efficiency and yield. The heat sink has better heat transfer properties than those of the pin fin because it has a higher surface area to volume ratio than that of the pin fin. The current study investigates the effect of heat sinks in passive pyramid solar still under two water depths (11 and 30 mm) on the hourly yield, accumulated yield, and efficiency of the distiller. Three cases were compared: conventional solar still (CSS), regular distribution of heat sinks (DHS), and grouped heat sinks in the middle of the solar still basin (GHS). In addition, the effect of atmospheric parameters such as solar radiation, UV index, humidity, dry bulb temperature, and ambient temperature on the solar still parameters such as water, vapor, cover, and feedwater temperature is investigated. Unexpectedly, heat sinks weakly affect the performance of solar still. Therefore, the conclusion of the previous studies that the finned absorber has a favorable impact on the solar still performance is not general and needs further investigation. The highest thermal efficiency was observed for the DHS and GHS at 30-mm water depth, where the efficiency was 35%.

Vertical GaN Power MOSFET with Integrated Fin-Shaped Diode for Reverse Conduction

A vertical GaN power MOSFET featuring an integrated fin-shaped non-junction diode (FDMOS) is proposed to improve reverse conduction and switching characteristics. Its static and dynamic characteristics are studied and analyzed by Sentaurus TCAD simulation. Compared with the conventional MOSFET (Con. MOS) with a body diode as a freewheeling diode (FWD), the FDMOS uses the integrated fin-shaped diode to reverse conduction, and thus, a low reverse turn-on voltage V_ON of 0.66 V is achieved, with a decreasing of 77.9%. Moreover, the Q_rr of the FDMOS is reduced to 1.36 μC from 1.64 μC of the Con. MOS, without the minority carrier injection. The gate charge (Q_GD) of the FDMOS is significantly reduced because the fin structure reduces the gate area and transforms some part of C_GD to C_GS, and thus, a low switching loss is realized. The Q_GD, the turn-on loss (E_on) and the turn-off loss (E_off) of the FDMOS are decreased by 56.8%, 33.8% and 53.8%, respectively, compared with those of the Con. MOS. In addition, the FDMOS is beneficial to reduce the parasitic inductance and the total chip area compared with the conventional method of using an externally connected Schottky diode as an FWD.

A comprehensive series of Irx cluster mutants reveals diverse roles in facial cartilage development

Proper function of the vertebrate skeleton requires the development of distinct articulating embryonic cartilages. Irx transcription factors are arranged in co-regulated clusters that are expressed in the developing skeletons of the face and appendages. IrxB cluster genes are required for the separation of toes in mice and formation of the hyoid joint in zebrafish, yet whether Irx genes have broader roles in skeletal development remains unclear. Here, we perform a comprehensive loss-of-function analysis of all 11 Irx genes in zebrafish. We uncover conserved requirements for IrxB genes in formation of the fish and mouse scapula. In the face, we find a requirement for IrxAb genes and irx7 in formation of anterior neural crest precursors of the jaw, and for IrxBa genes in formation of endodermal pouches and gill cartilages. We also observe extensive joint loss and cartilage fusions in animals with combinatorial losses of Irx clusters, with in vivo imaging revealing that at least some of these fusions arise through inappropriate chondrogenesis. Our analysis reveals diverse roles for Irx genes in the formation and later segmentation of the facial skeleton.

Evidence of multi-decadal behavior and ecosystem-level changes revealed by reconstructed lifetime stable isotope profiles of baleen whale earplugs

Biological time series datasets provide an unparalleled opportunity to investigate regional and global changes in the marine environment. Baleen whales are long-lived sentinel species and an integral part of the marine ecosystem. Increasing anthropogenic terrestrial and marine activities alter ocean systems, and such alterations could change foraging and feeding behavior of baleen whales. In this study, we analyzed δ¹³C and δ¹⁵N of baleen whale earplugs from three different species (N = 6 earplugs, n = 337 laminae) to reconstruct the first continuous stable isotope profiles with a six-month resolution. Results of our study provide an unprecedented opportunity to assess behavioral as well as ecological changes. Abrupt shifts and temporal variability observed in δ¹³C and δ¹⁵N profiles could be indicative of behavior change such as shift in foraging location and/or trophic level in response to natural or anthropogenic disturbances. Additionally, five out of six individuals demonstrated long-term declining trends in δ¹³C profiles, which could suggest influence of emission of depleted ¹³CO₂ from fossil fuel combustion referred to as the Suess effect. After adjusting the δ¹³C values of earplugs for the estimated Suess effect and re-evaluating δ¹³C profiles, significant decline in δ¹³C values as well as different rate of depletion suggest contribution of other sources that could impact δ¹³C values at the base of the food web.

Zebrafish can regenerate endoskeleton in larval pectoral fin but the regenerative ability declines

We show for the first time endoskeletal regeneration in the developing pectoral fin of zebrafish. The developing pectoral fin contains an aggregation plate of differentiated chondrocytes (endochondral disc; primordium for endoskeletal components, proximal radials). The endochondral disc can be regenerated after amputation in the middle of the disc. The regenerated disc sufficiently forms endoskeletal patterns. Early in the process of regenerating the endochondral disc, epithelium with apical ectodermal ridge (AER) marker expression rapidly covers the amputation plane, and mesenchymal cells start to actively proliferate. Taken together with re-expression of a blastema marker gene, msxb, and other developmental genes, it is likely that regeneration of the endochondral disc recaptures fin development as epimorphic limb regeneration does. The ability of endoskeletal regeneration declines during larval growth, and adult zebrafish eventually lose the ability to regenerate endoskeletal components such that amputated endoskeletons become enlarged. Endoskeletal regeneration in the zebrafish pectoral fin will serve as a new model system for successful appendage regeneration in mammals.

Time dependent ultrastructural alterations on the skin, eye, barbel and fins of the spawn of Clarias batrachus (Linn. 1758) exposed to UV-B radiation

Present study highlighted the ultramicroscopic (SEM) alterations of the skin, eye, barbel, and fins of spawn of an air-breathing teleost (Clarias batrachus, Linn. 1758) induced by UV-B radiation (280-320 nm) at a dose (@4.07 × 10^-20J/photon/m²) under the time-frame of 5, 10 and 15 min/d in the laboratory condition for the periods of 5 and 10 days. Limnological parameters revealed no significant changes throughout the period of experimentation which were measured by PCS Testr 35 Multi-Parameter. Morphometric analysis revealed that during the extended exposure period of 10 days the spawn size and weight were reduced as analysed through Specific Growth Rate (SGR). SGR values in terms of weight for 5 and 10 days under 3 time-frames were 17.12%, 12.52%, 11.46% and 9.09%, 6.43%, 6.09% respectively, which revealed a declined trend along with the exposure days. In the skin of C. batrachus, the compact regular orientation of the stratified epithelial cells and mucous cells became distorted and the microridges and double-ridged structures showed destruction and fragmentations. The body striations and microfolds became shrinked and swollen and finally degenerated to form a mass. The distribution of mucous cells throughout the epidermis was disorganised and releasing secretory contents on the surface through small pores. Appearance of huge quantity of biogenic semi-hexagonal plate like crystals (guanine platelets) on the skin surface of the body was the most significant observations during UV-B radiation. In the developmental phases the eyeball showed shrinkage loosing normal regular concave structure and to become a dome-shaped one. The supportive connective infoldings became loosened. The choroid coat displayed deformities and the iris deformed the pupil. The fibroblast on the epithelium and melanocytes depicted dispersed arrangement. The pairs of ventral barbels near the mouth depicted the presence of taste buds that became severely damaged exposing the sensory as well as neuroepithelial cells. Compact regular arrangement of the SECs was completely destroyed leaving long and deep channels inbetween them; the disintegrated concentric MRs also showed a mass.

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

BACKGROUND

Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored.

RESULTS

We produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes, coupled with stably maintained lineage-specific DNA methylation. The epigenetic signatures also reveal many novel regeneration-specific enhancers, which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map, and a knockout of a predicted upstream regulator disrupts normal regeneration, validating our prediction.

CONCLUSION

Our study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. In contrast, chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis.

RA Signaling in Limb Development and Regeneration in Different Species

This chapter brings together data on the role of retinoic acid (RA) in the embryonic development of fins in zebrafish , limbs in amphibians , chicks , and mice, and regeneration of the amphibian limb . The intention is to determine whether there is a common set of principles by which we can understand the mode of action of RA in both embryos and adults. What emerges from this synthesis is that there are indeed commonalities in the involvement of RA in processes that ventralize, posteriorize, and proximalize the developing and regenerating limb . Different axes of the limb have historically been studied independently; as for example, the embryonic development of the anteroposterior (AP) axis of the chick limb bud versus the regeneration of the limb bud proximodistal (PD) axis . But when we take a broader view, a unifying principle emerges that explains why RA administration to embryos and regenerating limbs results in the development of multiple limbs in both cases. As might be expected, different molecular pathways govern the development of different systems and model organisms, but despite these differences, the pathways involve similar RA signaling genes, such as tbx5, meis, shh, fgfs and hox genes. Studies of developing and regenerating systems have highlighted that RA acts by being synthesized in one embryonic location while acting in another one, exactly as embryonic morphogens do, although there is no evidence for the presence of an RA gradient within the limb . What also emerges is that there is a paucity of information on the involvement of RA in development of the dorsoventral (DV) axis . A molecular explanation as to how RA establishes and alters positional information in all three axes is the most important area of study for the future.

The skeletal ontogeny of Astatotilapia burtoni - a direct-developing model system for the evolution and development of the teleost body plan

Background

The experimental approach to the evolution and development of the vertebrate skeleton has to a large extent relied on “direct-developing” amniote model organisms, such as the mouse and the chicken. These organisms can however only be partially informative where it concerns secondarily lost features or anatomical novelties not present in their lineages. The widely used anamniotes Xenopus and zebrafish are “indirect-developing” organisms that proceed through an extended time as free-living larvae, before adopting many aspects of their adult morphology, complicating experiments at these stages, and increasing the risk for lethal pleiotropic effects using genetic strategies.

Results

Here, we provide a detailed description of the development of the osteology of the African mouthbrooding cichlid Astatotilapia burtoni, primarily focusing on the trunk (spinal column, ribs and epicentrals) and the appendicular skeleton (pectoral, pelvic, dorsal, anal, caudal fins and scales), and to a lesser extent on the cranium. We show that this species has an extremely “direct” mode of development, attains an adult body plan within 2 weeks after fertilization while living off its yolk supply only, and does not pass through a prolonged larval period.

Conclusions

As husbandry of this species is easy, generation time is short, and the species is amenable to genetic targeting strategies through microinjection, we suggest that the use of this direct-developing cichlid will provide a valuable model system for the study of the vertebrate body plan, particularly where it concerns the evolution and development of fish or teleost specific traits. Based on our results we comment on the development of the homocercal caudal fin, on shared ontogenetic patterns between pectoral and pelvic girdles, and on the evolution of fin spines as novelty in acanthomorph fishes. We discuss the differences between “direct” and “indirect” developing actinopterygians using a comparison between zebrafish and A. burtoni development.

Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration

Background

Regeneration is an important biological process for the restoration of organ mass, structure, and function after damage, and involves complex bio-physiological mechanisms including cell differentiation and immune responses. We constructed four regenerative protein-protein interaction (PPI) networks using dynamic models and AIC (Akaike’s Information Criterion), based on time-course microarray data from the regeneration of four zebrafish organs: heart, cerebellum, fin, and retina. We extracted core and organ-specific proteins, and proposed a recalled-blastema-like formation model to uncover regeneration strategies in zebrafish.

Results

It was observed that the core proteins were involved in TGF-β signaling for each step in the recalled-blastema-like formation model and TGF-β signaling may be vital for regeneration. Integrins, FGF, and PDGF accelerate hemostasis during heart injury, while Bdnf shields retinal neurons from secondary damage and augments survival during the injury response. Wnt signaling mediates the growth and differentiation of cerebellum and fin neural stem cells, potentially providing a signal to trigger differentiation.

Conclusion

Through our analysis of all four zebrafish regenerative PPI networks, we provide insights that uncover the underlying strategies of zebrafish organ regeneration.

The role of HoxA11 and HoxA13 in the evolution of novel fin morphologies in a representative batoid (Leucoraja erinacea)

Background

Batoids exhibit unique body plans with derived fin morphologies, such as the anteriorly expanded pectoral fins that fuse to the head, or distally extended anterior pelvic fin lobes used for a modified swimming technique utilized by skates (Rajidae). The little skate (Leucoraja erinacea), exhibits both of these unique fin morphologies. These fin modifications are not present in a typical shark body plan, and little is known regarding the mechanisms underlying their development. A recent study identified a novel apical ectodermal ridge (AER) associated with the development of the anterior pectoral fin in the little skate, but the role of the posterior HoxA genes was not featured during skate fin development.

Results

We present the first evidence for HoxA expression (HoxA11 and HoxA13) in novel AER domains associated with the development of three novel fin morphologies in a representative batoid, L. erinacea. We found HoxA13 expression associated with the recently described novel AER in the anterior pectoral fin, and HoxA11 expression in a novel AER domain in the anterior pelvic fin that we describe here. We find that both HoxA11 and HoxA13 are expressed in claspers, and while HoxA11 is expressed in pelvic fins and claspers, HoxA13 is expressed exclusively in developing claspers of males. Finally, HoxA11 expression is associated with the developing fin rays in paired fins.

Conclusion

Overall, these results indicate that the posterior HoxA genes play an important role in the morphological evolution of paired fins in a representative batoid. These data suggest that the batoids utilize a unique Hox code, where the posterior HoxA genes exhibit distinct expression patterns that are likely associated with specification of novel fin morphologies.

Electronic supplementary material

The online version of this article (10.1186/s13227-017-0088-4) contains supplementary material, which is available to authorized users.

The evolutionary origin of digit patterning

The evolution of tetrapod limbs from paired fins has long been of interest to both evolutionary and developmental biologists. Several recent investigative tracks have converged to restructure hypotheses in this area. First, there is now general agreement that the limb skeleton is patterned by one or more Turing-type reaction–diffusion, or reaction–diffusion–adhesion, mechanism that involves the dynamical breaking of spatial symmetry. Second, experimental studies in finned vertebrates, such as catshark and zebrafish, have disclosed unexpected correspondence between the development of digits and the development of both the endoskeleton and the dermal skeleton of fins. Finally, detailed mathematical models in conjunction with analyses of the evolution of putative Turing system components have permitted formulation of scenarios for the stepwise evolutionary origin of patterning networks in the tetrapod limb. The confluence of experimental and biological physics approaches in conjunction with deepening understanding of the developmental genetics of paired fins and limbs has moved the field closer to understanding the fin-to-limb transition. We indicate challenges posed by still unresolved issues of novelty, homology, and the relation between cell differentiation and pattern formation.

A simple and non-invasive method for analyzing local immune responses in vivo using fish fin

Immunocompetence is an important parameter that reflects disease resistance in fish. Very few methods to examine immunocompetence in vivo have been developed, even for mammals. In the present study, we present a unique method for analyzing local immune responses using fish fin. We first demonstrated the migration of granulocytes to the site of zymosan injection in fin in a dose-dependent manner and that this could be easily observed macroscopically due to the fin membrane transparency. We also demonstrated phagocytic activity of accumulated leukocytes after zymosan administration and that almost all phagocytes were granulocytes. In addition, we succeeded to detect respiratory burst activity of granulocytes in vivo without any in vitro treatment of cells, indicating that our present method is suitable for the analysis of granulocyte phagocytic function in vivo. The method provides a unique tool applicable for fishes that possess transparent fins and may lead to better understanding of the mechanisms of local immune responses in fish.

Muscle development in the shark Scyliorhinus canicula: implications for the evolution of the gnathostome head and paired appendage musculature

BACKGROUND

The origin of jawed vertebrates was marked by profound reconfigurations of the skeleton and muscles of the head and by the acquisition of two sets of paired appendages. Extant cartilaginous fish retained numerous plesiomorphic characters of jawed vertebrates, which include several aspects of their musculature. Therefore, myogenic studies on sharks are essential in yielding clues on the developmental processes involved in the origin of the muscular anatomy.

RESULTS

Here we provide a detailed description of the development of specific muscular units integrating the cephalic and appendicular musculature of the shark model, Scyliorhinus canicula. In addition, we analyze the muscle development across gnathostomes by comparing the developmental onset of muscle groups in distinct taxa. Our data reveal that appendicular myogenesis occurs earlier in the pectoral than in the pelvic appendages. Additionally, the pectoral musculature includes muscles that have their primordial developmental origin in the head. This culminates in a tight muscular connection between the pectoral girdle and the cranium, which founds no parallel in the pelvic fins. Moreover, we identified a lateral to ventral pattern of formation of the cephalic muscles, that has been equally documented in osteichthyans but, in contrast with these gnathostomes, the hyoid muscles develop earlier than mandibular muscle in S. canicula.

CONCLUSION

Our analyses reveal considerable differences in the formation of the pectoral and pelvic musculatures in S. canicula, reinforcing the idea that head tissues have contributed to the formation of the pectoral appendages in the common ancestor of extant gnathostomes. In addition, temporal differences in the formation of some cranial muscles between chondrichthyans and osteichthyans might support the hypothesis that the similarity between the musculature of the mandibular arch and of the other pharyngeal arches represents a derived feature of jawed vertebrates.

A gene expression study of dorso-ventrally restricted pigment pattern in adult fins of Neolamprologus meeli, an African cichlid species

Fish color patterns are among the most diverse phenotypic traits found in the animal kingdom. Understanding the molecular and cellular mechanisms that control in chromatophore distribution and pigmentation underlying this diversity is a major goal in developmental and evolutionary biology, which has predominantly been pursued in the zebrafish model system. Here, we apply results from zebrafish work to study a naturally occurring color pattern phenotype in the fins of an African cichlid species from Lake Tanganyika. The cichlid fish Neolamprologus meeli displays a distinct dorsal color pattern, with black and white stripes along the edges of the dorsal fin and of the dorsal half of the caudal fin, corresponding with differences in melanophore density. To elucidate the molecular mechanisms controlling the differences in dorsal and ventral color patterning in the fins, we quantitatively assessed the expression of 15 candidate target genes involved in adult zebrafish pigmentation and stripe formation. For reference gene validation, we screened the expression stability of seven widely expressed genes across the investigated tissue samples and identified tbp as appropriate reference. Relative expression levels of the candidate target genes were compared between the dorsal, striped fin regions and the corresponding uniform, grey-colored regions in the anal and ventral caudal fin. Dorso-ventral expression differences, with elevated levels in both white and black stripes, were observed in two genes, the melanosome protein coding gene pmel and in igsf11, which affects melanophore adhesion, migration and survival. Next, we predicted potential shared upstream regulators of pmel and igsf11. Testing the expression patterns of six predicted transcriptions factors revealed dorso-ventral expression difference of irf1 and significant, negative expression correlation of irf1 with both pmel and igsf11. Based on these results, we propose pmel, igsf11 and irf1 as likely components of the genetic mechanism controlling distinct dorso-ventral color patterns in N. meeli fins.

Functional morphology and hydrodynamics of backward swimming in bluegill sunfish, Lepomis macrochirus

Most teleost fishes, like the bluegill sunfish Lepomis macrochirus, have multiple flexible fins that are used as modifiable control surfaces. This helps to make fish highly maneuverable, permitting behaviors like reversing direction of motion and swimming backwards without having to rotate body position. To answer the question of how fish swim backwards we used high-speed videography and electromyography to determine the kinematics and muscle activity necessary to produce reverse-direction propulsion in four bluegill sunfish. We found that, in contrast to slow forward swimming, low-speed backward swimming is a multi-fin behavior, utilizing the pectoral, dorsal, anal, and caudal fins. The pectoral fins alternate beats, each fin broadly flaring on the outstroke and feathered on the instroke. The dorsal fin and dorsal portion of the caudal fin move out of phase as do the anal fin and ventral portion of the caudal fin. Electromyography of muscles in the pectoral, dorsal, anal, and caudal fins demonstrated bilateral activation when these fins changed direction, suggesting that fins are stiffened at this time. In addition to backward propulsion by the pectoral fins, particle image velocimetry revealed that the dorsal and anal fins are capable of producing reverse momentum jets to propel the fish backward. Because teleost fishes are statically unstable, locomotion at slow speeds requires precise fin control to adequately balance torques produced about the center of mass. Therefore, the kinematics of backward swimming may be the result of compensation for rolling, pitching, and yawning instability. We suggest that asymmetric pectoral fin activity with feathering during adduction balances rolling instability. The ventral to dorsal undulatory wave on the caudal fin controls pitch instability and yaw instability encountered from pectoral-driven backward locomotion. Thrust generation from the dorsal and anal fins decreases the destabilizing effect of the long moment arm of the tail in backward swimming. Thus, backward locomotion at slow speed is not simply the reverse of slow forward swimming.

The phantoms of a high-seven - or - why do our thumbs stick out?

The earliest tetrapods had hands and feet with up to eight digits but this number was subsequently reduced during evolution. It was assumed that lineages with more than five digits no longer exist but investigations of clawed-frogs now indicate that they posses a rudimentary or atavistic sixth digit in their hindlimb. A recent reevaluation of the stem tetrapod Ichthyostega predicts that its seven digits evolved from two different types of ancestral fin radials, pre-axial and post-axial. In this context we now ask the question, should we consider a pre-axial origin of the thumb as reason for its unique genetic signature?

Size and Orientation Effects on the Kinetics and Structure of Nickelide Contacts to InGaAs Fin Structures

The rapid development of ultrascaled III-V compound semiconductor devices urges the detailed investigation of metal-semiconductor contacts at nanoscale where crystal orientation, size, and structural phase play dominant roles in device performance. Here, we report the first study on the solid-state reaction between metal (Ni) and ternary III-V semiconductor (In0.53Ga0.47As) nanochannels to reveal the reaction kinetics, formed crystal structure, and interfacial properties. We observe a size-dependent Ni surface diffusion dominant kinetic process that gradually departs to a volume diffusion process as the Fin width increases, as properly depicted with our Fin-specific growth model. The interfacial relationship was found to be Ni4InGaAs2 (0001) ∥ In0.53Ga0.47As (111) with a single Ni4InGaAs2 phase whose [0001] axis exhibit a peculiar rotation away from the nickelide/InGaAs interface due to surface energy minimization. This crystalline interfacial relationship is responsible for introducing a uniaxial height expansion of 33% ± 5% in the formed nickelide segments. Further, the nickelide formation resulted in both in-plane and out-of-plane compressive strains in the Fin channels, significantly altering the In0.53Ga0.47As energy band-edge structure near the interface with a peak bandgap energy of ∼1.26 eV. These timely observations advance our understanding and development for self-aligned contacts to III-V nanochannels and for engineering new processes that can maximize their device performance.

Macrophages modulate adult zebrafish tail fin regeneration

Neutrophils and macrophages, as key mediators of inflammation, have defined functionally important roles in mammalian tissue repair. Although recent evidence suggests that similar cells exist in zebrafish and also migrate to sites of injury in larvae, whether these cells are functionally important for wound healing or regeneration in adult zebrafish is unknown. To begin to address these questions, we first tracked neutrophils (lyzC⁺, mpo⁺) and macrophages (mpeg1⁺) in adult zebrafish following amputation of the tail fin, and detailed a migratory timecourse that revealed conserved elements of the inflammatory cell response with mammals. Next, we used transgenic zebrafish in which we could selectively ablate macrophages, which allowed us to investigate whether macrophages were required for tail fin regeneration. We identified stage-dependent functional roles of macrophages in mediating fin tissue outgrowth and bony ray patterning, in part through modulating levels of blastema proliferation. Moreover, we also sought to detail molecular regulators of inflammation in adult zebrafish and identified Wnt/β-catenin as a signaling pathway that regulates the injury microenvironment, inflammatory cell migration and macrophage phenotype. These results provide a cellular and molecular link between components of the inflammation response and regeneration in adult zebrafish.

Transcriptional components of anteroposterior positional information during zebrafish fin regeneration

Many fish and salamander species regenerate amputated fins or limbs, restoring the size and shape of the original appendage. Regeneration requires that spared cells retain or recall information encoding pattern, a phenomenon termed positional memory. Few factors have been implicated in positional memory during vertebrate appendage regeneration. Here, we investigated potential regulators of anteroposterior (AP) pattern during fin regeneration in adult zebrafish. Sequence-based profiling from tissues along the AP axis of uninjured pectoral fins identified many genes with region-specific expression, several of which encoded transcription factors with known AP-specific expression or function in developing embryonic pectoral appendages. Transgenic reporter strains revealed that regulatory sequences of the transcription factor gene alx4a activated expression in fibroblasts and osteoblasts within anterior fin rays, whereas hand2 regulatory sequences activated expression in these same cell types within posterior rays. Transgenic overexpression of hand2 in all pectoral fin rays did not affect formation of the proliferative regeneration blastema, yet modified the lengths and widths of regenerating bones. Hand2 influenced the character of regenerated rays in part by elevation of the vitamin D-inactivating enzyme encoded by cyp24a1, contributing to region-specific regulation of bone metabolism. Systemic administration of vitamin D during regeneration partially rescued bone defects resulting from hand2 overexpression. Thus, bone-forming cells in a regenerating appendage maintain expression throughout life of transcription factor genes that can influence AP pattern, and differ across the AP axis in their expression signatures of these and other genes. These findings have implications for mechanisms of positional memory in vertebrate tissues.

Novel polymorphisms in UTR and coding region of inducible heat shock protein 70.1 gene in tropically adapted Indian zebu cattle (Bos indicus) and riverine buffalo (Bubalus bubalis)

Due to evolutionary divergence, cattle (taurine, and indicine) and buffalo are speculated to have different responses to heat stress condition. Variation in candidate genes associated with a heat-shock response may provide an insight into the dissimilarity and suggest targets for intervention. The present work was undertaken to characterize one of the inducible heat shock protein genes promoter and coding regions in diverse breeds of Indian zebu cattle and buffaloes. The genomic DNA from a panel of 117 unrelated animals representing 14 diversified native cattle breeds and 6 buffalo breeds were utilized to determine the complete sequence and gene diversity of HSP70.1 gene. The coding region of HSP70.1 gene in Indian zebu cattle, Bos taurus and buffalo was similar in length (1,926 bp) encoding a HSP70 protein of 641 amino acids with a calculated molecular weight (Mw) of 70.26 kDa. However buffalo had a longer 5' and 3' untranslated region (UTR) of 204 and 293 nucleotides respectively, in comparison to Indian zebu cattle and Bos taurus wherein length of 5' and 3'-UTR was 172 and 286 nucleotides, respectively. The increased length of buffalo HSP70.1 gene compared to indicine and taurine gene was due to two insertions each in 5' and 3'-UTR. Comparative sequence analysis of cattle (taurine and indicine) and buffalo HSP70.1 gene revealed a total of 54 gene variations (50 SNPs and 4 INDELs) among the three species in the HSP70.1 gene. The minor allele frequencies of these nucleotide variations varied from 0.03 to 0.5 with an average of 0.26. Among the 14 B. indicus cattle breeds studied, a total of 19 polymorphic sites were identified: 4 in the 5'-UTR and 15 in the coding region (of these 2 were non-synonymous). Analysis among buffalo breeds revealed 15 SNPs throughout the gene: 6 at the 5' flanking region and 9 in the coding region. In bubaline 5'-UTR, 2 additional putative transcription factor binding sites (Elk-1 and C-Re1) were identified, other than three common sites (CP2, HSE and Pax-4) observed across all the analyzed animals. No polymorphism was found within the 3'-UTR of Indian cattle or buffalo as it was found to be monomorphic. The promoter sequences generated in 117 individuals showed a rich array of sequence elements known to be involved in transcription regulation. A total of 11 nucleotide changes were observed in the promoter sequence across the analyzed species, 3 of these changes were located within the potential transcription factor binding domains. We also identified 4 microsatellite markers within the buffalo HSP70.1 gene and 3 microsatellites within bovine HSP70.1. The present study identified several distinct changes across indicine, taurine and bubaline HSP70.1 genes that could further be evaluated as molecular markers for thermotolerance.

Life-long preservation of the regenerative capacity in the fin and heart in zebrafish

The zebrafish is a widely used model animal to study the regeneration of organs, such as the fin and heart. Their average lifetime is about 3 years, and recent studies have shown that zebrafish exhibit aging-related degeneration, suggesting the possibility that aging might affect regenerative potential. In order to investigate this possibility, we compared regeneration of the fin and heart after experimental amputation in young (6-12 month old) and old (26-36 month old) fish. Comparison of recovery rate of the caudal fin, measured every two or three days from one day post amputation until 13 days post amputation, show that fins in young and old fish regenerate at a similar rate. In the heart, myocardium regeneration and cardiomyocyte proliferation occurred similarly in the two groups. Moreover, neo-vascularization, as well as activation of fibroblast growth factor signaling, which is required for neo-vascularization, occurred similarly. The epicardial tissue is a thin layer tissue that covers the heart, and starts to express several genes immediately in response to injury. The expression of epicardial genes, such as wt1b and aldh1a2, in response to heart injury was comparable in two groups. Our results demonstrate that zebrafish preserve a life-long regenerative ability of the caudal fin and heart.