Directed capillary ingrowth has long been considered synonymous with tumor vascularization. However, the vasculature of primary tumors and metastases is not necessarily formed by endothelial cell sprouting; instead, malignant tumors can acquire blood vessels via alternative vascularization mechanisms, such as intussusceptive microvascular growth, vessel co-option, and glomeruloid angiogenesis. Importantly, in response to anti-angiogenic therapies, malignant tumors can switch from one vascularization mechanism to another. In this article, we briefly review the biological features of these mechanisms and discuss on their significance in medical oncology. Above this size, the so-called angiogenic switch occurs; currently, anti-angiogenic therapies are based on this assumption. In this article, we review and compare our data on the vascularization mechanisms of primary and metastatic tumors with the findings of other groups. We also discuss the potential reasons for failure of anti-angiogenic therapies [Angiogenesis refers to the proliferation of vascular cells  and the increase of vessel density. It has a pivotal role in the nutrition of tumors. In the 1970s, Folkman et al. [herapies , 3.The two basic forms of angiogenesis are endothelial sprouting  and intuTwo models of sprouting angiogenesis have been described. According to the first model, interendothelial contacts of the venules closest to the tumors become weakened . This phThe second model suggests that interendothelial contacts remain intact, and after the degradation of the basement membrane, polarized endothelial cells migrate into the connective tissue . During Intussusceptive angiogenesis  is another mode to increase vessel density. This process enhances the complexity and density of the vessel network, thus providing additional surface for further vessel sprouting . IntussuThe formation of intraluminal pillars may also occur by another mechanism, the first step of which is the formation of endothelial bridges in the lumen. Here, degradation of the basement membrane takes place, and bridging endothelial cells attach to connective tissue collagen bundles and transport them through the lumen. The collagen bundles are covered by endothelial cells; thus, initially, the nascent pillars are built up by two endothelial cells and a single collagen bundle. Fibroblasts migrate into this pillar and synthesize additional connective tissue, which results in pillar maturation . Of noteNumerous schematic depictions in various studies suggested that, during vascularization, the nearby vessels grow into the tumor , 9, 10. In clinical oncology, treatment of metastases is a great challenge. Angiogenesis is a possible target for the treatment of tumors. Since the most frequent sites for metastasis formation  contain dense capillary networks and a relatively small amount of connective tissue, it is likely that vascularization of metastases develops differently from primary tumors.3). We found no new vessel formation in the close vicinity of tumors. Vessel density and bromodeoxyuridine (BrdU) labeling index of vascular cells did not change significantly. Tumors became vascularized exclusively by the incorporation of host vessels  are characteristics mainly of primary brain tumors, but they appear in brain metastases and in other tumors as well . GBs acqVermeulen et al.  describeWe examined experimental liver metastases that were produced by the injection of Lewis lung carcinoma cells into the spleen of C57Bl/6 mice. In this model, tumor cells reached the liver via the portal vein and formed colonies. Our studies on anaplastic Lewis lung carcinoma liver metastases showed that tumor cells migrated in the space of Disse during the invasion, at the tumor periphery, thereby detaching the endothelial cells from their basement membrane  . EndotheOur analysis of the pushing-type metastases produced by using C38 colon carcinoma cells showed that even in the early stages of metastasis development, proliferation of myofibroblasts and accumulation of connective tissue occur in the close vicinity of the metastases . In paraFinally, it is noteworthy that in neither sinusoidal (replacement) nor pushing-type metastases does angiogenesis take place in the peritumoral liver parenchyma.In earlier studies, we found that the default growth type of experimental lung metastases is the “flow” of proliferating tumor cells from alveolus to alveolus  Fig. 3aa3a, b. TCells of undifferentiated tumors enter into the alveolar walls, and during their invasion/migration they detach pneumocytes from the surface of capillaries Fig. c. As a rPolarized tumor cells of well-differentiated C38 colon tumor do not migrate back into the alveolar walls from the alveolar space; instead, they induce a desmoplastic reaction in the alveolar wall. During this reaction, the fibroblasts present in the alveolar wall are transformed into smooth muscle actin (SMA)-expressing and connective tissue collagen-synthesizing myofibroblasts. Alveolar walls being incorporated into the tumor gradually widen, resulting in the development of connective tissue columns . The structure of these columns corresponds completely to the structure of connective tissue columns in the liver metastases of this same tumor Fig. b. The acIn organs with dual blood supply (the liver and lung), the origin of the blood supply of metastases has been long debated. Most analyses have been done in the liver . These experiments were performed by the injection of colored resin or India ink into the vasculature –27. HoweWe conclude that the incorporation of both the preexisting host vasculature (which can be modified by the tumor) and the newly formed vessels plays an important role in the vascularization of tumors. The incorporation process is basically biomechanical in nature. We think that anti-angiogenic therapies should be given mainly to patients with primary tumors in which endothelial proliferation is present. The perimetastatic region cannot be targeted by anti-angiogenic therapies because angiogenesis does not occur in the adjacent host tissues of tumor metastases (possibly because of the lack of sufficient connective tissue). However, when sufficient connective tissue is synthesized in the more central part of the lesions in a later phase of metastasis development, intratumoral angiogenesis is possible. This requires the presence of connective tissue cells in the target organ that are able to transform into collagen-synthesizing myofibroblasts.


Free innervated muscle transfer (FMT) achieves functional restoration following not only traumatic brachial plexus injury, but also intractable rare upper limb disorders, such Hopkins' syndrome, myoplasia in arthrogryposis and radition neuropathy. I introduce our current experience of FMT for these disorders.Hopkins syndrome is a rare cause of poliomyelitis-like paralysis affecting one or more extremities after an acute attack of asthma. The exact etiology of Hopkins syndrome is not known. Two children developed acute asthma followed by complete flaccid paralysis of the the upper extremity. They underwent staged reconstruction using FMT. Rigorous postoperative physiotherapy was carried out to achieve a good functional outcome. At recent follow-up, they were able to effectively use the reconstructed hand for most of their daily activities. They had good control and could perform 2-handed activities. The selection of a suitable operative treatment and suitable donor nerves is critical, and there are no clear guidelines in the literature. FMT can be effectively employed in similar cases to restore grasping function.Arthrogryposis is a collective term applied to a variety of different syndromes characterized by nonprogressive, multiple joint contractures present at birth due to neurogenic, myopathic (amyoplasia), or connective-tissue disorders. The most serious impairment of amyoplasia in the upper extremity is an inability to flex the elbow due to extension contracture of the elbow. The ability to flex one elbow is essential to enable a child to become functionally independent with self-feeding and self-care of the face and hair; extension of the other elbow is necessary for independent toileting. Active elbow flexion is the definitive goal of surgical intervention.Multiple procedures, including triceps transfer, pectoralis major transfer, latissimus dorsi transfer, and the Steindler flexorplasty, have been used to provide active elbow flexion in patients with arthrogryposis. However, these conventional procedures do not always provide satisfactory long-term function and may result in a decreased arc of elbow flexion and in flexion contracture because of weakness of the donor muscles.We present the long-term results of a functioning free muscle transfer with use of the gracilis muscle for restoration of elbow flexion in three patients with arthrogryposis.Radiation-induced brachial plexopathy is a delayed complication of radiation treatment for tumors involving the neck and chest area and is progressive. A 56 year-old woman presented to us with loss of elbow flexion and weak wrist and finger extension 15 years after she received external beam radiation to the left chest, axilla, and supraclavicular region for the treatment of breast cancer. She was managed with a gracilis free muscle transfer for elbow flexion and hand prehension. By 2 years after surgery she regained elbow range of motion of 40 to 110 degrees and improved her hand function. She was able to perform her activities of daily living. Her Disabilities of the Arm, Shoulder, and Hand Score improved from 56 to 20.


Coronoid process hyperplasia is an uncommon finding, characterized by an enlargement of the coronoid process, causing a mechanical obstacle by its interposing in the posterior portion of the maxilla or zygomatic arch.The article presents a case report of a bilateral coronoid process hyperplasia in a 3-year-old girl demonstrated with inability to open the mouth and restricted jaw movement. Panoramic x-ray and 3-dimensional computed tomographic reconstruction showed bilateral elongation of the coronoid processes associated with deformation of the mandibular condyle with no involvement of the articular space. A coronoid resection by intraoral approach was done, followed by an aggressive physiotherapy. A considerable improvement in mouth opening of 30 mm was achieved. We strongly suggest early surgical treatment of coronoid hyperplasia to recover morphology and function consequently to reduce skeletofacial deformities in young patients.The article presents a clinical and surgical case of bilateral coronoidectomy in a 3-year-old girl, with retrognathic mandible. The diagnosis of bilateral coronoid process hyperplasia was confirmed, and the surgical treatment was under general anesthesia, with nasotracheal intubation guided by a nasofiber endoscope, using an intraoral approach. The coronoid process hyperplasia is an uncommon finding, characterized by an enlargement of the coronoid process, causing a mechanical obstacle by interposition of this structure in the posterior portion of the maxilla or zygomatic arch. The most important feature of this condition is a mouth opening reduction , 2. Its Among conventional radiographic image techniques, the oblique posteroanterior, modified Town’s for condyles and computed tomography with three-dimensional reconstructions are used for accurately evaluation of the coronoid process .This case report is about a patient with bilateral mandibular coronoid process hyperplasia treated with coronoidectomy, followed with intensive physical therapy. To the best of our knowledge, this is the youngest patient so far reported with such bilateral anomaly.A 3-year-old girl was referred to the Clinic for Maxillofacial Surgery with inability to open her mouth, restricted jaw movement and limited mastication. Convex profile, severely retrognathic mandible and absence of chin button were present. Intraoral examination revealed mouth opening of only 1-2 mm .Preoperative assessment included anamnesis, radiographic and physical investigation. Parents could not recollect the time of onset of mouth opening restriction. Child’s photos from the first months of life showed no restrictions of the mouth opening, indicating that the condition was not caused by any trauma during delivery.Panoramic radiographs and 3-dimensional computed tomographic reconstruction confirmed bilateral elongation of the coronoid processes associated with deformation of the mandibular condyle with no involvement of articular space . It appeUsing Bard-Parker blade, intraoral incisions  were made bilaterally along the buccal mucosa (anterior border - margo anterior of mandible) at the level of occlusal plane and extended posteriorly up to the anterior faucial pillars.The coronoid processes were approached through the incision along with stripping of the temporalis attachment on the anterior border of ramus of mandible and cutting of tendon attachments .The first step of osteotomy was made to the right coronoid process of mandible . After uCoronoidectomy was done through an intraoral approach followed with mouth opening of 30 mm (satisfactory distance between upper and lower lip of the mouth). Surgical procedure was performed under general anesthesia with nasotracheal intubation, guided by a nasofiber endoscope.Alginate impressions were taken intra-operatively to fabricate a splint. Postoperatively the parents were advised for intensive daily mandibular physiotherapy with device TheraBite.One week after surgery, rehabilitation was begun using a TheraBite 3-5 times a day for 5-10 minutes. Two and six weeks postoperatively, muscular stretching and forced mouth opening under general anesthesia were performed.As a final result, a mouth opening of 25 mm was achieved, enabling the patient to consume a normal diet and take care of her teeth .The patient was follow-up postoperatively for at regular intervals after three months, six months, nine months and one year and we found no reduction of mouth opening established with previous treatment.Ethical approval: All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.Coronoid hyperplasia negatively influences growth and development of the jaws and teeth; because of the facial deformity, which worsens with growth, psychosocial development of the patient is affected as well , 6.Etiopathogenesis of bilateral forms of coronoid hyperplasia has been seen limited and has not yet been described, it should be to both developmental and endocrine abnormalities, followed by a familiar pattern of inheritance.The poor specificity of signs and symptoms associated with this type of bilateral coronoid hyperplasia present problems of differential diagnosis.Three-dimensional computed tomography with reconstruction is necessary and fundamental for differentiation of the coronoid hyperplasia from other conditions such: ankilosis, coronoid neoplasms (chondroma or osteochondroma), trauma and thickened but not elongated coronoid processes . This reIntraoral and extraoral approach are described in literature, with intraoral being more recommended for preventing external scars and facial nerve injury . We perfIntensive postoperative physical therapy is critical for clinical success; treatment failure is usually due to inadequate physical therapy. In this case the device TheraBite was used , 10.We strongly suggest early surgical treatment to recover morphology and function, consequently reducing skeletofacial deformities in young patients.In conclusion, coronoid process hyperplasia depending on their location and extent can cause mandibular hypomobility. Setting the diagnosis of coronoid hyperplasia as soon as possible and its distinguishing from other forms of ankylosis by using three-dimensional computed tomography is very important. While a considerable level of mouth opening reduction and restricted mandible’s function is present, a coronoidectomy by intraoral approach followed by an intensive physiotherapy (begin between 1-2 weeks after surgery with stretching and passive movements) gives satisfactory results in treatment of this condition.Coronoid process hyperplasia is an uncommon finding, characterized by an enlargement of the coronoid process, causing a mechanical obstacle by its interposing in the posterior portion of the maxilla or zygomatic arch. Panoramic x-ray and 3-dimensional computed tomographic reconstruction in our manuscript showed bilateral elongation of the coronoid processes associated with deformation of the mandibular condyle with no involvement of the articular space. We strongly suggest early surgical treatment of coronoid hyperplasia to recover morphology and function consequently to reduce skeletofacial deformities in young patients.


Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire.Clusters of orthologous mitochondrial protein-coding genes (MitoCOGs) were constructed from all available mitochondrial genomes and complemented with nuclear orthologs of mitochondrial genes. With minimal exceptions, the mitochondrial gene complements of eukaryotes are subsets of the superset of 66 genes found in jakobids. Reconstruction of the evolution of mitochondrial genomes indicates that the mitochondrial gene set of the last common ancestor of the extant eukaryotes was slightly larger than that of jakobids. This superset of mitochondrial genes likely represents an intermediate stage following the loss and transfer to the nucleus of most of the endosymbiont genes early in eukaryote evolution. Subsequent evolution in different lineages involved largely parallel transfer of ancestral endosymbiont genes to the nuclear genome. The intron density in nuclear orthologs of mitochondrial genes typically is nearly the same as in the rest of the genes in the respective genomes. However, in land plants, the intron density in nuclear orthologs of mitochondrial genes is almost 1.5-fold lower than the genomic mean, suggestive of ongoing transfer of functional genes from mitochondria to the nucleus.The MitoCOGs are expected to become an important resource for the study of mitochondrial evolution. The nearly complete superset of mitochondrial genes in jakobids likely represents an intermediate stage in the evolution of eukaryotes after the initial, extensive loss and transfer of the endosymbiont genes. In addition, the bacterial multi-subunit RNA polymerase that is encoded in the jakobid mitochondrial genomes was replaced by a single-subunit phage-type RNA polymerase in the rest of the eukaryotes. These results are best compatible with the rooting of the eukaryotic tree between jakobids and the rest of the eukaryotes. The land plants are the only eukaryotic branch in which the gene transfer from the mitochondrial to the nuclear genome appears to be an active, ongoing process.The online version of this article (doi:10.1186/s12862-014-0237-5) contains supplementary material, which is available to authorized users. The mitochondrion is a membrane-bounded organelle that performs multiple, pivotal roles in the eukaryotic cell. The primary function of the mitochondria is the synthesis of ATP through the oxidative electron transport chain but mitochondria are also involved in other biological functions such as intracellular signaling including induction of programmed cell death -3. AlthoRhodobacterales . The analyzed complete genomes grouped by taxonomy are listed in Additional file 36,120 protein sequences from 2,486 complete mitochondrial genomes with representatives from all the major eukaryotic supergroups were used to generate the MitoCOGs. Incomplete kinetoplastid proteomes were obtained from GOBASE  and all MitoCOGs were generated using a slightly modified procedure for COG construction that was described previously ,49. BrieDue to the strict requirement of the 50% coverage threshold and only a single best hit in each species, the COG construction software missed shorter sequences and paralogs. The initial clusters were expanded to include these sequences as follows. A position-specific scoring matrix (PSSM) for each initial cluster was created by aligning cluster member protein sequences using MUSCLE , followeThe strict requirements for COG creation also result in underclustering when a COG is split into two or more clusters. To remedy over-splitting, the expanded clusters were merged using a modification of the procedure described previously . The PSSAncestral gene content evolution of mitochondrial genomes was reconstructed using the Count software . For a gIdentifying the nuclear-encoded orthologs of MitoCOGs is a non-trivial task because nuclear genomes encompass genes coding for homologs of mitochondrial proteins  that can be difficult to distinguish from bona fide mitochondrial proteins. In order to identify the true mitochondrial orthologs, MitoCOGs PSSMs were searched using PSI-BLAST  against complete proteomes of selected eukaryotes (nuclear-encoded), alpha-proteobacteria, cyanobacteria and archaea . The matrices of intron absence/presence along with the corresponding species tree were used as the input data for the DOLLOP program of the PHYLIP package . This prPhylogenetic analyses were performed using (1) only mitochondrion-encoded proteins and (2) both mitochondrion-encoded and nuclear-encoded proteins. Alpha-proteobacterial sequences were used as outgroup. Protein sequences of individual MitoCOGs (and nuclear-encoded proteins for the second dataset) were aligned with the alpha-proteobacterial sequences using MUSCLE and the poorly aligned columns were removed as previously described . The aliMalawimonas, Naegleria, Andalucia and Reclinomonas). However, there are at least 8 mitochondrial genomes with coverage below 50%  were generated as described under Methods. Altogether, 140 MitoCOGs were delineated from 34,751 mitochondrial-encoded proteins. Additional file MitoCOGs . The lowAdditional file C. reinhardtii  subunits alpha (rpoA), beta (rpoB), beta-prime (rpoC), and sigma (rpoD), ribosomal large subunit proteins RPL1, RPL27 and RPL34, RPL35 and COX15 (the latter two present only in A. goyodi), SecY protein involved in co-translational membrane translocation of proteins (absent only in A. goyodi), and the 6 uncharacterized proteins. The RNAP function in other eukaryotes is relegated to a single subunit bacteriophage-type polymerase that is encoded in the nuclear genome [Emiliania huxleyi, and the ribosomal small subunit protein RPS16 in amoeba Vermamoeba (formerly Hartmannella) vermiformis and the excavate Malawimonas jakobiformis. The MutS [V. vermiformis also encodes the ribosomal large subunit protein RPL19 and elongation factor EF-Tu that are otherwise present only in jakobids. Notably, the genes for RPS16 and RPL19 in V. vermiformis show similar order to that in the trmD operon of several alpha-proteobacteria and other bacteria  between the unikonts and bikonts ,55, (2) From the Count analysis, we estimated the average propensity of loss (transfer) for individual mitochondrial proteins and multisubunit complexes (by averaging the number of lineages that have lost the genes that constitute the complex). The lineages that have lost individual genes and complexes are listed in Additional file Lineage-specific transfer of mitochondrial genes to the nuclear genome results in patchy phyletic patterns of MitoCOGs when only genes present in mitochondrial genomes are included Figure . PutativStrongylocentrotus purpuratus had the maximum number of nuclear orthologs (33) that mapped to 21 MitoCOGs. However, most of the redundant hits could be due to errors in gene prediction [Chlamydomonas reinhardtii has the largest number of nuclear-encoded orthologs (24) followed by Arabidopsis thaliana (23). C. reinhardtii is exceptional in that some of the genes that encode proteins involved in oxidative phosphorylation that are typically encoded in the mitochondrial genome have been transferred to the nuclear genome. In contrast, another green alga, Ostreococcus tauri, encodes most of its genes in the mitochondrial genome, with only 7 identifiable genes encoded in the nuclear genome. Naegleria gruberi whose mitochondrial gene content is the closest to the most gene-rich jakobid mitochondrial genomes in our dataset had only 3 identifiable nuclear-encoded orthologs. The analyzed dataset included 5 nuclear genomes from species that lack regular mitochondria: Encephalitozoon cuniculi, Entamoeba histolytica, Giardia lamblia, Nosema ceranae, and Trichomonas vaginalis. None of these species encompass any identifiable orthologs of mitochondrial genes.The phyletic distributions of MitoCOGs and their nuclear-encoded orthologs are shown jointly in Figure ediction . Otherwiediction . Indeed,ediction . HoweverAmong the MitoCOGs, ATP3 shows the widest phyletic distribution of nuclear orthologs (47 of the 55 species) followed by SDH2 (46 of the 55 species) . However, only one such duplication, that of the RPL2 gene, is conserved in two species . Such high variability of the double nuclear-mitochondrial encoding is consistent with the hypothesis that functional gene transfer from the mitochondrial genome to the nuclear genome is an ongoing process in land plants [A. thaliana genes that are duplicated in the mitochondrial and nuclear genomes, the encoded protein sequences are more than 99% identical, and so are the sequences of the only pair of duplicated genes in O. tauri. However, several of these nuclear genes, the high sequence similarity with the mitochondrial counterparts notwithstanding, contain introns that obviously have been inserted after the transfer .For 14 genes, both nuclear and mitochondrial versions were identified in the same genome  in the nuclear orthologs of mitochondrial genes with the mean intron densities of the respective nuclear genomes which were taken from the previous analysis  Figure . The intThe majority of the introns (47.5%) were of phase 0, followed by phase 1 (29.7%) and phase 2 (22.7%)  and asymmetric . Symmetric 0–0 exons are most common in eukaryotic genomes followed by 1–0 exons . Althoug–1, 2–2 aChlamydomonas reinhardtii (73%), Cryptococcus neoformans (72%) and Caenorhabditis elegans (72%), which belong to plantae, fungi, and metazoa groups, respectively. Among distant lineages of eukaryotes, there are few shared introns in nuclear orthologs of mitochondrial genes. For example, only 3 of the 105 introns in these genes are shared between human and Arabidopsis, in a sharp contrast to approximately 30% conserved introns in ancestral eukaryotic genes.Introns are mostly conserved among closely related species with fewer species-specific introns and even fewer shared introns between distant lineages Figure . The speWe applied Dollo parsimony to reconstruct the most parsimonious scenario for the evolution of gene structure ,102, i.eUnder the resulting parsimonious scenario, only 21 (3%) introns were already present in the nuclear orthologs of the mitochondrial genes of the last common ancestor of the analyzed eukaryotic species Figure . This loThe MitoCOGs described here are a resource for analysis of the genes that are present in at least one sequenced mitochondrial genome but in many eukaryotes have been transferred to the nuclear genome. Altogether there are 70 such genes, not counting genes of numerous mobile elements that are integrated in mitochondrial genomes of many plants, fungi and diverse unicellular eukaryotes. These genes represent a relatively small subset of the endosymbiont-derived component of the mitochondrial proteome as most of the retained endosymbiont genes have been transferred to the nucleus at an early stage of the evolution of eukaryotes and have not been identified in the mitochondrial genome of any extant eukaryotes ,108,109.Vermamoeba vermiformis and Acanthamoeba castellanii that is missing in the excavates. The history of RPS16 conceivably is the most striking case of massive parallel gene loss in mitochondrial evolution. Given the lack of evidence of reintroduction of genes into mitochondrial genomes and the alpha-proteobacteria-like arrangement of the r-protein genes, including RPS16, in V. vermiformis and A. castellanii  are unique to the jakobids. Thus, it appears most likely that the mitochondrial gene set of jakobids is close to the ancestral state of the eukaryotic mitochondrial genome. Clearly, this ancestral state is far removed from the full genome of the alpha-proteobacterial ancestor of the mitochondria: judging by the smallest genomes of the extant alpha-proteobacteria that might be affiliated with the proto-mitochondrial lineage, such as Rickettsia and Pelagibacter ubique, the genome of the original endosymbiont encompassed about 1000 genes if not more. The great majority of these genes were either lost or transferred to the nuclear genome, conceivably in a rapid succession, at early stages of the evolution of eukaryotes, shortly after the endosymbiosis. The mitochondrial genome of the jakobid lineage apparently experienced the minimum amount of gene transfer from the already substantially reduced mitochondrial genome of the LECA.Although most mitochondrial genomes contain many fewer genes than that of jakobidsNaegleria gruberi. Under the jakobid topology, the ATP3 gene was transferred to the nucleus twice, namely, at the branch between the excavates and the rest of the eukaryotes and at the base of the Euglena-Trypanosome branch. The gene encoding the translation factor EF-Tu also contains 2 intron positions that are conserved in more than one eukaryotic supergroup where nuclear copies of the gene have been identified. In this case, however, the evolutionary scenario is complicated by the fact that EF-Tu is encoded in the mitochondrial genome not only in jakobids but also in V. vermiformis. The only conceivable evolutionary scenario for this gene includes early transfer of a copy of the EF-Tu gene to the nucleus followed by extended co-existence of the nuclear and mitochondrial copies, with multiple parallel losses of the latter.Perhaps, the most notable and enigmatic aspect of mitochondrial evolution is the apparent replacement of the four genes for bacterial RNAP subunits that are present in the mitochondrial genomes of jakobids and by inference were contained in the mitochondrial genome of the LECA as well by a single subunit, phage-type RNAP in the rest of the eukaryotes ,70. The Bryophyta as well. The causes of ongoing functional gene transfer from the mitochondrial genome to the nuclear genome and HGT in land plants but apparently not in other groups of eukaryotes remain unclear.An ongoing process of functional gene transfer from the mitochondrial genome to the nuclear genome was observed in angiosperms ,77,78. TComparative analysis of thousands of mitochondrial genomes across the diversity of eukaryotes validates a previously observed, non-trivial pattern: with very few exceptions, the mitochondrial gene complements of eukaryotes are overlapping subsets of the largest mitochondrial gene set of 66 genes that is found in jakobids. Reconstruction of the evolution of mitochondrial genomes suggests a gene set that was slightly larger than that of jakobids for the last common ancestor of the extant eukaryotes. This superset of mitochondrial genes is much smaller than the gene repertoires of even the simplest known α-proteobacteria and thus represents an intermediate stage in the evolution of eukaryotes that followed extensive loss of genes from the endosymbiont genome at a stage antedating the last common ancestor. The subsequent evolution of mitochondrial genomes in different lineages of eukaryotes consisted primarily in the transfer of ancestral genes, in particular those encoding ribosomal proteins, to the nuclear genomes. Much of this gene transfer occurred in parallel in different lines of evolution. This reconstruction of mitochondrial genome evolution implies that jacobids are the earliest-branching group of eukaryotes that retains some key features of the ancestral endosymbiont such as the multisubunit RNA polymerase. Although not popular previously, this scenario is compatible with the results of some recent phylogenetic studies, and at present appears most plausible.ftp://ftp.ncbi.nih.gov/pub/koonin/MitoCOGs.Supporting data are available via


The influence of plant traits on forest fire behaviour has evolutionary, ecological and management implications, but is poorly understood and frequently discounted. We use a process model to quantify that influence and provide validation in a diverse range of eucalypt forests burnt under varying conditions. Measured height of consumption was compared to heights predicted using a surface fuel fire behaviour model, then key aspects of our model were sequentially added to this with and without species-specific information. Our fully specified model had a mean absolute error 3.8 times smaller than the otherwise identical surface fuel model (p < 0.01), and correctly predicted the height of larger (≥1 m) flames 12 times more often (p < 0.001). We conclude that the primary endogenous drivers of fire severity are the species of plants present rather than the surface fuel load, and demonstrate the accuracy and versatility of the model for quantifying this. Plants may affect forest fire behaviour by influencing the quantity and flammability of surface fuel, the three dimensional structure of the forest, and through the flammability of their live parts. The effect of variation in dominant species on surface fine litter load is well established  and evidet al for example characterised sites with broader leaves as less flammable due to a positive correlation between leaf width and time to ignition [The role of leaf traits in influencing fire behaviour via flammability remains uncertain. While strong evidence exists for the influence of chemistry, moisture and morphology on leaf flammability –13 and lignition , while oignition ,5.Given these uncertainties, it has been argued that fire behaviour models can disregard the influence of certain flammable properties of plant parts. Alexander and Cruz  for instOur aim was to show that stand-level characteristics of fire behaviour could be successfully predicted on the basis of knowledge of the flammable properties of plant species and the interaction of these properties that arise from considering the three dimensional arrangement of whole plants and their relevant, flammable features, such as leaves and stems. Specifically, we predicted flame height using a modelling approach that accounted for the arrangement of plants and their flammable parts plus the influence of the morphology of these parts on flammability. We then tested predictions derived from the model against field estimates of char height or the height to which leaves are consumed by fire following a wildfire, in a range of forest sites across a mountainous region of south eastern Australia.Plant traits can potentially affect fire characteristics at the whole plant and stand scale via several fundamental processes. First, the properties of individual leaves such as size, shape, moisture content and chemical composition –13,23 deIn this study we tested the hypothesis that flammability properties of leaves will significantly affect characteristics of fire at the scale of a forest stand via the mechanisms listed above. Specifically, we examined how variations in flame propagation and resultant height of flames across multiple strata of plants within forest stands emerge from variations in characteristics of component species and their inherent effects on flammability and the spatial arrangement of leaves. We explored this using a comparative modelling approach to examine the sensitivity of predicted variations in the propagation and dimensions of flames to different representations of the structure and composition of eucalypt forest stands. We compared predictions from the models against ground-measured and remotely-sensed estimates of fire severity, for which we used height of combustion in vegetation as an index of flame dimensions . Char heOur measurements were taken within the perimeter of a major wildland fire which burned across diverse terrain, forest and weather conditions. These comparisons allowed us to test whether incorporation of leaf characteristics of individual species and their effects on ignitability, combustibility, sustainability, heat transfer and wind profiles, improved predictions of flame dimensions.We conducted our study in two stages to quantify the influence of plant species composition and structural manifestation on forest fire behaviour. First, we proposed and tested a site-based biophysical, mechanistic model of fire behaviour as influenced by the species-driven properties of forest structure and leaf traits, and in the second we analysed the model outputs to identify the conditions under which leaf traits were important determinants of fire behaviour, and which groups of traits had the most influencehttps://github.com/pzylstra/ffm_cpp/tree/Zylstra2016, and further explanation is provided in The Forest Flammability Model ,36,  determines the dimensions of the heat plume and the nature of the temperature gradient within it . The durLeaves ignite if the period of flame duration produced by the donor leaf exceeds the time to ignition for the receiver. This is a function of both the temperature at that point in the plume and the ignitability of the leaf . Leaf igThis process is repeated at escalating scales from leaf to branch, plant and plant stratum.Combustibility and ignitability therefore interact in the model to determine the depth of ignition (distance from the flame at which leaves can be ignited), which together with the density of foliage gives the number of leaves ignited for each one-second time step. The angle at which the burning plume intersects a plant crown or stratum defines a plume pathway or potential depth of foliage that can be ignited. This angle is adjusted at each time step as wind speed and flame dimensions affect the flame angle, so that the plume pathway evolves over time. The total number of leaves burning in a time step is the sum of leaves burning in the previous step plus those newly ignited, minus the leaves that have extinguished as determined by their sustainability properties. The resulting flame length for that step is a function of the number of leaves burning, the combustibility of those leaves and physical processes of heat transfer and air entrainment between them.In vegetation with multiple plant strata, the severity of a fire expressed as the height of combustion  will be Plants in strata above a flame but not burning may influence the behaviour of the fire via effects on wind speed in the burning strata. Such effects will be a function of the amount of shelter provided by the overhead foliage, which in the FFM is modelled from the Leaf Area Index (LAI) calculated from leaf size, density on the branch, ramification and spacing of branches in the non-burning strata above the flames, along with the physical size and spacing of plant crowns. These effects on wind may, in turn, affect the angle of the heat plume and thereby the length of the plume pathway, the length of flame produced, and the angle and distance to receiver leaves . Thus leThe FFM is initiated using a model of surface fire spread that produces a pilot flame to potentially ignite above-ground fuel strata. Species-specific leaf traits are known to affect surface fire behaviour (see introductory discussion), however at this point no model exists that incorporates these effects. In the absence of such a model, this study uses the Burrows model  for thisWe validated the model by investigating whether variations in structure and species composition of forest stands affected stand-level flame dimensions as predicted. We compared outputs from three modelling treatments with field observations of the height of combustion (height above the ground at which leaves and stems were consumed by fire) as a proxy for flame height in eucalypt forests of south-eastern Australia. The comparative modelling approach enabled us to systematically contrast predictions of stand-level flame dimensions produced by models that treated the representation of fuel with successively increasing levels of complexity. These ranged from surface litter fuel only to full consideration of structural arrangement and species-level leaf dimensions Tables  and 2. TWe tested the null hypothesis by comparing the three sets of predictions against estimates of height of combustion across a range of sites burnt by a major wildland fire in south-eastern Australia . MountaiThree scenarios were modelled to address the hypothesis that vegetation structure and leaf traits are important to fire behaviour; these were:Surface fuel load only (F)–no structural or leaf traits effects of standing plants considered;Surface fuel load and stand structure (FS)–as for (F), but considering structural effects of above ground plants but not effects of leaf traits; andSurface fuel load, stand structure and leaf traits (FSL)–as for (FS), but also considering leaf traits of component species.Eucalyptus species of varying height  and estPredictions of flame height for each site were produced using site-specific exogenous conditions  and addrAll treatments used wind speed adjusted for overstorey sheltering by vegetation, and this was summarised for each site using the modelled wind reduction factors (WRF: above-canopy wind speed / wind speed at 1.5 m above ground level) as approximations of the full vertical wind-speed profiles used by the FFM for each site.The predictions produced from each approach were then compared with the site-based upper and lower limits of flame height to determine whether the inclusion of leaf traits and their arrangement within various strata improved the accuracy of predictions.1 for a subset of sites where measured flames were at least 1m in height. The MAE, PCP and PCP1 were then compared between successive inclusions of structure and leaf traits using paired t-tests to determine whether any apparent improvements were statistically significant for those statistics. This approach was chosen in preference to a more standard nested-model comparison, as in addition to identifying the better treatment, it quantified the accuracy of each with statistics that we considered meaningful to model application.The absolute error (AE) of predictions was estimated to identify treatment bias, and the mean absolute error (MAE) to provide a natural and unambiguous measure of model performance . To bettIn the second stage, we examined how the inclusion of leaf traits affected the relative importance of the three key mechanisms represented in the FFM  in predicting estimated flame height. This was done by comparing the way that overall flame height changed between the FS and FSL treatments in response to parameters representing the three key processes, along with a range of other influences representing characteristics of the study sites, weather at the time of burning and other measures of vegetation/fuel structure .To achieve this, we performed Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis  to identLASSO regression was used to simultaneously fit models and select those subsets of predictors having most influence, with the coefficients for other predictors being forced to zero. The response variable was predicted flame height under FS minus that under FSL. Additive regression models were fitted using the “glmnet” package  for R 5, with thTrial regressions showed that there was substantial variation in the predictors chosen when the fitted model was selected using minimum prediction error (“min” rule) in repeated runs of the cross-validation procedure. In contrast, only one predictor (Delta donor Fh) was present in models selected with the one-standard-error rule (“1se” rule). This indicated a single dominant variable with a number of secondary variables of much less influence, whose inclusion depended on the random allocation of sites to training and test folds during cross-validation. Since our purpose was interpretation rather than prediction, we did not wish to simply discard these secondary variables. To investigate them further we undertook an ensemble regression analysis in which 1000 LASSO models were selected using the “min” rule, and the frequency of inclusion of each predictor in the fitted additive models was recorded along with statistics  describing the characteristic regression coefficients for each.Observed fire severity ranged from surface (i.e. consumption of litter fuel only) at two sites to crown fire at four sites . EstimatThe successive inclusion of information on structure and other plant attributes improved the accuracy of predictions of flame dimensions relative to field estimates , Table 71 was 9.50 times higher (p < 0.001), which was indicative of the inability of F to predict these flames.The inclusion of vegetation structural attributes without leaf trait information (FS) resulted in the prediction of large flames not previously predicted on the basis of F. However, in several sites where small flames were estimated, very large flames were predicted . As a re1 were respectively 2.25 and 12.00 times higher for FSL than for F (p < 0.001 for both), and 1.16, 1.26 times larger than for FS , removing most of the false predictions of large flames . This prThe most frequent (>70%) predictors included in the LASSO regression analyses were donor flammability (delta donor flame height), wind velocity, overstorey shelter (delta sum LAI) and dead fuel moisture content (DFMC); with delta canopy LAI and slope affecting the regression at moderate (>30%) frequency . ReceiveDonor flammability, DFMC and slope had the effect of reducing flame height predicted using species leaf traits (FSL) relative to predictions based on structure only (FS) . Thus we omitted consideration of effects of leaf variations on the flammability of surface litter in the current study Exploration of such effects will be an important priority for future research.Variations in surface-fuel variables had almost no explanatory power for larger (≥1 m) flames but produced satisfactory predictions when flames were small. This suggests that surface fuel variables were important drivers of low intensity fires in these forests, but ignition of whole plants was the main cause of larger flames. Flame propagation across gaps between plants to produce larger flames was either limited or enabled by plant size and spacing and the flammability of leaves. Species-specific leaf traits are known to affect surface fire behaviour but models for representing these effects on the mass and packing of surface litter and subsequent fire behaviour are lacking. In addition, leaves of the Acacia, Bossiaea, Bursaria, Carex, Eucalyptus, Leptospermum spp.) resulting from inclusion of specific leaf traits , resulting from the inclusion of leaf traits, were associated with the overall reductions in predicted flame height for these sites  was more likely to over-predict flame height. This was exacerbated on steep slopes, when dead fuel was moister and when wind speeds were slower. In contrast, a model without leaf traits (FS) tended to under-predict flame height when LAI and consequent wind reduction were overestimated. Leaf traits therefore become increasingly important for predicting large flames under dry, windy conditions, and to a lesser extent, on shallow slopes.Bossiaea foliosa was greater than the mean values used in FS, so that they ignited and thus propagated flames into the midstorey using FSL , including under-prediction and over-prediction  and relasing FSL . Thinneright see . Thus thin situ micro-climates that are likely to alter the probability of fire e.g. [Our study found that for these sites, plant traits were more important for predicting flame height than was surface fuel load. This has important implications for fire ecology and management as it verifies some elements of a potential feedback relationship between fire behaviour and fire ecology that have been identified in conceptual models e.g. ,64 but lire e.g. ; howeverWhile it is well known that particular fire regimes can select for certain species and thus alter the structure and composition of plant communities –69; our The results of the study indicate the need to more widely examine implications of forest structure and composition for fire behaviour. For example, the need to explore a wide range of plant trait variation in global vegetation models has been advocated ,74. AssoAn important limitation of the FFM is the time to ignition sub-model , which dIt is likely that a considerable proportion of the error in flame height predictions may be due the use of photogrammetric measurement of fuels, standard live moisture values, and the predictions of weather parameters from weather stations not located on the fire ground. Considerations of such sources of uncertainty and error will be a priority for future studies.While we have demonstrated that the FFM more accurately predicted variations in flame length as a function of variations in the composition and structure of some eucalypt forests, further work is required to explore the accuracy of the FFM in other communities, and its capacity to represent other aspects of fire behaviour such as rate of spread. Such insights will help to determine the types of applications where the use of a complex model such the FFM may be most viable, given the demands of parametrisation of fuel compared with other fire behaviour models.The inclusion of species level traits in a modelling framework that represented flammability of plant parts and the resultant capacity of flames to propagate through their three dimensional arrangement (i.e. as represented in the FFM) considerably enhanced the ability to predict flame height in eucalypt forest communities. Conventional approaches to modelling fire behaviour based on the mass of surface litter and simple measures of above-ground fuel strata may therefore be unable to predict aspects of fire behaviour that arise from variations in forest composition. The FFM mechanistically explains the effects of plant traits on fire behaviour, thereby providing a basis for exploring the way in which variations in community composition can affect fire behaviour in the short-term and, perhaps, longer term fire regimes. The structure of the model also allows for the integration of new theoretical work on flammability and fire physics, providing an adaptive framework that can provide both direction for new research and application to evolutionary, ecological and management questions.S1 Fig(PDF)Click here for additional data file.S2 Fig(PDF)Click here for additional data file.S3 Fig(PDF)Click here for additional data file.S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S3 Table(PDF)Click here for additional data file.S4 Table(PDF)Click here for additional data file.S5 Table(PDF)Click here for additional data file.S6 Table(PDF)Click here for additional data file.


Colossoma macropomum), Amazonian fish species considered promising for fish farming, has been the subject of extensive genetic research with biotechnology focus. This study aimed to express the cDNA encoding GH tambaqui (tGH) in the methylotrophic yeast Pichia pastoris. The nucleotide sequence of cDNA tGH, previously isolated by Sousa (2009) [P. pastoris and obtained by chemical synthesis. It was then cloned into the cloning vector pUC19 followed by subcloning into expression and secretion vector pPIC9 with the endonucleases Eco RI and NotI. The recombinant plasmid named pPIC-tGH was linearized and inserted into host by electroporation. Recombinant clones were selected in medium auxotrophic for histidine. The expression of recombinant protein was induced by methanol addition during 96 hours occurred in shake flasks. The culture supernatant was analyzed on SDS-PAGE gel and expression of tGH was confirmed by Western blotting. The analysis of the supernatant revealed in both phenotype Mut+ and Muts the presence of a protein band of approximately 23 kDa, which was confirmed to be the tGH recombinant by Western blotting using monoclonal antibody against histidine tail C- terminal. The expression of tGH started already first 24 hours and was sustained throughout the induction period, lasted up to 120 h. These results are similar to of Li et al. [Cyprinus carpio) in P. pastoris and observed that from the first 24 hours of induction the recombinant protein was already present in the medium, and time 72 and 96 hours corresponded to the peak of expression. These results demonstrate that GH tambaqui can be successfully expressed in P. pastoris. The tambaqui, for their economic importance, so far was the first Amazonian fish species to have GH expressed in heterologous system, the first step in the production of GHs of other important species for aquaculture regional and national. In the future, tambaqui recombinant GH should be analyzed for their efficiency in accelerating the growth of tambaqui towards the possible use in aquaculture production, which represent progress and innovation in technologies of cultivation of fish Amazonian.Genetic studies involving the search, cloning and expression of genes encoding proteins involved in important physiological processes and advantageous features of the economic standpoint have become the biotechnology research increasingly promising. Due to its zootechnical importance, the encoding gene of growth hormone (GH) of various fish species have been isolated, cloned and expressed in heterologous expression systems. The tambaqui (a 2009) , was opt009 , was


In southern Tibet, ongoing vertical and horizontal motions due to the collision between India and Eurasia are monitored by large numbers of global positioning system (GPS) continuous and campaign sites installed in the past decade. Displacements measured by GPS usually include tectonic deformation as well as non-tectonic, time-dependent signals. To estimate the regional long-term tectonic deformation using GPS more precisely, seasonal elastic deformation signals associated with surface loading must be removed from the observations. In this study, we focus on seasonal variation in vertical and horizontal motions of southern Tibet by performing a joint analysis of GRACE (Gravity Recovery and Climate Experiment) and GPS data, not only using continuous sites but also GPS campaign-mode sites. We found that the GPS-observed and GRACE-modeled seasonal oscillations are in good agreements, and a seasonal displacement model demonstrates that the main reason for seasonal variations in southern Tibet is from the summer monsoon and its precipitation. The biggest loading appears from July to August in the summer season. Vertical deformations observed by GPS and modeled by GRACE are two to three times larger than horizontal oscillations, and the north components demonstrate larger amplitudes than the east components. We corrected the GPS position time series using the GRACE-modeled seasonal variations, which gives significant reductions in the misfit and weighted root-mean-squares (WRMS). Misfit ( The ongoing crustal deformation of the Tibetan Plateau results from the collision between India and Eurasia. The Indian plate has been moving northward at a rate of ~4 cm/year with respect to Siberia. About half of the continental convergence is accommodated by crustal shortening across the southern edge of the Tibetan Plateau ,2,3,4. AIt is well known that the present-day deformation manifest geodetically in the Himalaya and southern Tibet contains not only signals associated with tectonic processes such as earthquake deformation but also transient processes caused by surface hydrology . SeasonaThe elastic deformation due to surface water transport is detected in both GPS ,19,20,21Earlier studies focused on vertical components of cGPS sites in consideration of the larger signal in the vertical and the need for continuous observations to compare independent measures of seasonal variation. Recently, horizontal components of cGPS time series also have been examined to constrain surface loading changes in combination with the vertical components ,38,39. GFormer and current cGPS and campaign stations in southern Tibet  are analWe used the GIPSY/OASIS software (version goa-5.0) to process the GPS data and estimate station coordinates for all sites in precise point positioning (PPP) mode. The data analysis follows the procedures described in Fu and Freymueller . We usedWe estimated PPP solutions for all sites shown in We employed the GRACE Level-2 Release-05 (RL05) of monthly gravity field products, GRACE Satellite only Model (GSM) solution files, provided by the University of Texas Center for Space Research (UTCSR). Those GSM files are in the form of spherical harmonics coefficients (SHCs) up to degree 60, from August 2002 to February 2015. Displacements due to the changing mass load can be computed from spherical harmonic coefficients for the surface load and the load Love numbers ,48,49.WRMSThe summer monsoon brings significant rainfall that inevitably induces additional mass loading on southern Tibet and the Himalaya, and previous studies have demonstrated that rainfall in the summer is the biggest source of seasonal variations in the GPS time series. In order to remove hydrology-induced deformation signals and better measure tectonic phenomena, we used GRACE measurements to remove the hydrological signals from the time series based on the seasonal loading model mentioned above. In the following sections, we will analyze the effects of seasonal variations in the vertical and horizontal directions. We validate the approach using the continuous GPS sites, and then apply it to the campaign data.GRACE-modeled seasonal variations for the vertical deformation can be used to correct seasonal effects in the GPS time series. We choose the continuous GPS sites LHAZ and KKN4  as examples. In  et al. [Most earlier studies focused on the vertical deformation because of its large amplitude. Wahr  et al.  demonstr et al. . To charThe reduction of WRMS in the north component is about 30%, but in the east component is not so good, about two-thirds of the sites’ reduction in the east component is about 5%–10%, and for the other third, it is even negative (meaning increased WRMS after correction). This reflects a combination of the smaller horizontal signal, especially in the east component, possible systematic errors in the GPS data, and the spatial smoothing of the GRACE data.Seasonal variations also exist in campaign GPS sites if the observations are not made at the same time of year, but they cannot be removed except using an external calibration model because there are too few observations to estimate seasonal corrections from the data, neglecting the seasonal impact can bias the estimated linear velocities . We can The good results for cGPS sites indicate that the same method could be used for GPS campaign measurements. We tested this hypothesis for campaign GPS sites, and The 2015 Mw7.8 Gorkha earthquake occurred in late April . In the Postseismic deformation is time dependent, and post-earthquake GPS displacements often display a logarithmic or exponential decay with time, or a similar time-dependent relaxation. The shape of these relaxation curves is widely used to infer the dominant postseismic mechanisms and time scales. The presence of seasonal loading deformation can distort the apparent shape of these relaxation curves, and potentially impact the conclusions drawn about postseismic processes or time scales. It is noted that the seasonal variation over a period of a half-year containing the summer amounts to 15 mm in the vertical component and 5 mm in the horizontal component. For the Nepal earthquake, the seasonal displacements will substantially change the apparent rate of postseismic deformation if they are not removed using an appropriate model, and thus bias estimates of postseismic relaxation parameters and mechanisms. Thus it is prerequisite to deduce realistic surface displacements from GPS time series to delineate its spatial pattern and estimate the amount.Toward that end, we used the GRACE-based seasonal model to correct the original time series for a half-year duration . The N-SPostseismic vertical displacements will depend on the site location and the dominant mechanism of postseismic deformation. GRACE-modeled displacements due to seasonal hydrological loading show high correlation with GPS observed seasonal variations, which confirms that the hydrological mass cycle is the main cause of seasonal deformation in southern Tibet. From the shape of modeled seasonal variations, we find that the biggest surface mass anomaly appears during July to August and the smallest one appears during February. This indicates that the summer monsoon and induced rainfall are the most important reason of the loading change in southern Tibet.We use the misfit and WRMS reduction after removing the GRACE-modeled seasonal deformation from the GPS position time series to evaluate the correction of seasonal effects by GRACE. For CMONOC II sites, in vertical component, the range of misfit reduction is from 15%–38%, for CMONOC I sites (with longer time series), it is from 20%–56%. The north component has larger seasonal variations than the east component, and the correlation between GPS-observed and GRACE-modeled seasonal displacement shows that the correlation in the north component is better than in the east component.The results presented in this paper demonstrate that loading models based on GRACE measurements can effectively remove the seasonal signals in both continuous and campaign-mode GPS observations in this region with very large seasonal hydrological loading. We also demonstrate that the seasonal variation from a GPS site in southern Tibet agrees well with the seasonal oscillations estimated from the GRACE time-variable monthly gravity field. The seasonal variations in the GPS time series amount to up to 15 mm in vertical direction that cannot be ignored when GPS series in this region are used to determine postseismic deformation associated with the 2015 Nepal earthquake. Further studies should consider the spatial smoothing impact of GRACE solutions, the effects of non-tidal ocean, snow, groundwater, permafrost freezing and thawing in the GPS position time series, the GIA effect, which can cause both gravity change and vertical motion, the long-term vertical deformation in this region , as well


Understanding the responses of ecological communities to human-induced perturbations is crucial for establishing conservation goals. Ecological communities are dynamic entities undergoing fluctuations due to their intrinsic characteristics as well as anthropogenic pressures varying over time. In this respect, long-term studies, based on large spatial and temporal datasets, may provide useful information in understanding patterns and processes influencing the communities’ structure. Theoretical evidence suggests that a role of biodiversity is acting as a compensatory buffer against environmental variability by decreasing the temporal variance in ecosystem functioning and by raising the level of community response to perturbations through the selection of better performing species. Therefore, the spatial and temporal changes in the specialization of the community components may be used as an effective tool to monitor the effects of natural and anthropogenic alterations of the environment in dynamic systems. We examined the temporal dynamics of macroinvertebrate community structure in the hyperhaline habitat of Tarquinia Saltworks . We aimed at: (i) investigating the relationships between the level of community specialization and the alterations of the environment across fourteen years; (ii) comparing the ability of aggregate community parameters such as the average abundance vs. species specialization in describing patterns of community composition.p < 0.01) only in the community inhabiting the saltwork basin closely connected to the sea, characterized by the highest environmental variation . Here we found marine species like Modiolus adriaticus , Neanthes irrorata , and Amphiglena mediterranea , which inhabited the saltworks during the halt period but disappeared during the subsequent eutrophication phase. Conversely, species specialization showed a significant decrease for each sampled community in the presence of habitat degradation and a recovery after ecological restoration. The widest fluctuations of specialization were recorded for the community inhabiting the saltwork basin with the highest long-term environmental variability.We arranged the data in three sub-sets according to three periods, each characterized by different environmental conditions. The mean abundance of sampled macroinvertebrates showed a significant change (Recent advances have shown how the increased temporal and spatial variability of species’ abundance within the communities may be a signal of habitat disturbance, even in the absence of an apparent decline. Such approach could also be used as a sensitive monitoring tool, able to detect whether or not communities are subjected to increasing biotic homogenization. Also, the increased functional similarity triggered by habitat degradation may impact on species at higher trophic levels, such as the waterbirds wintering in the area or using it as a stopover during migration. Theoru Levins). For inu Levins. Conversu Levins.Monitoring the changes in community structure may help detect early signals of environmental disturbance. In particular, a number of studies highlight a link between environmental fluctuations, including anthropogenic disturbance, and biodiversity loss,6. EcoloA crucial issue is the trade-off between specialist and generalist species in explaining the functioning of key ecosystem processes,14, as sCoastal aquatic ecosystems are extremely dynamic habitats where the environmental variations occur over small temporal and spatial scales. In partIn this study, we examined long-term changes on the macroinvertebrate community composition of a hyperhaline habitat represented by halted saltworks. The aim was to test whether and how the level of community specialization could be impacted by both natural fluctuations and human-induced alterations in the environment. About fourteen years of monitoring activities have been divided into three main temporal blocks centered on a three-year period of management activities aimed at restoring the water circulation between the saltwork basins. The variation of aggregate community properties (i.e. average abundance) and species specialization  were calculated for each array of environmental conditions to check for the reliability of such metrics in describing patterns of community structure. Also, the trends of these metrics were analyzed in basins characterized by different environmental variability to verify their sensitivity in comparing coarse- vs. fine-grained environmental changes.r = 0.96), followed by the dissolved oxygen concentration (r = -0.24). Both parameters showed marked fluctuations  dropped from 21 taxa during the halt period to 14 during the eutrophication phase and then recovered up to 24 taxa during the post-recovery.The benthic macroinvertebrates recovered are listed in Table H = 17.85, p < 0.01) and the degree of specialization (SSI)  of sampled macroinvertebrates in basin 1 across the entire study period. However, the communities in basins 2 and 3 did not show any significant variation of abundance , although SSI significantly varied in both communities . The distribution of SSI across the three periods followed the same trend in all sampled communities . This was consistent with the pattern of points separation in the nMDS plot  as observed by the pattern of points separation in the nMDS ordination plot  by considering this latter as a proxy of the degree of specialization,31,32.Most of the environmental variability within the study area was due to the spatial and temporal fluctuations in the level of salinity, which is confirmed as the main driving force in the structuring process of both benthic communities and species genetic structuring in the study site,34. ThisHowever, an approach simply relying on abundance may fail in describing spatial and temporal variability of communities, as their composition may be altered without detectable changes in aggregate community properties,38. MeasOur findings well fall within this framework even if we recorded steady values of abundance and only a slight increase in richness with 24 taxa sampled during the post-recovery against 21 from the halt period. We found that assessing the variation of the degree of species specialization highlights significant changes within the sampled communities and puts temporal and spatial variability of these traits in relation with environmental impacts. Indeed, our longitudinal study across fourteen years includes abrupt changes , which clearly distinguish periods characterized by different environmental conditions and disturbance. In partModiolus adriaticus , Neanthes irrorata , and Amphiglena mediterranea  that inhabited the saltworks during the halt period but disappeared during the subsequent eutrophication phase  unfit for either the eutrophic or managed  habitat.Temporal changes in the degree of specialization were associated with the environmental fluctuations, which were in turn related to the different states of the habitat. The highest values of SSI have been recorded during the halt period, when the lack of human intervention modified the environmental conditions allowing marine species to enter and colonize the saltworks. Accordingly, basin 1 was the one with the highest values of SSI. This basin is closely connected to the sea and we found marine species like e Table . Howevere Table . This isTherefore, our results underline that maintaining a remarkable level of spatial and temporal heterogeneity is crucial for guaranteeing a high biodiversity at the community level. Indeed, the replacement of specialists by more generalist species may have severe consequences on both community and ecosystem functioning  and decrease the synchronization and variability in the responses to disturbance between connected communities.As coastal aquatic environments are among the most dynamic and impacted ecosystems, it is crucial to understand how the spatial and temporal variability of the environmental conditions may alter the biological composition of their animal communities. Here, we showed how changes in the frequency and magnitude of environmental fluctuations relate to the degree of temporal specialization of macroinvertebrate species in spatially defined communities. Our results support recent advances in the biotic homogenization of biodiversity, which rLong term studies linking environmental changes and impacts to the marine community structure are now emerging-45, whilThese results have conservation implications, since an increased replacement of specialists by more generalist species may be the signal of a deterioration of environmental conditions, which reduces the spatial and temporal variability of communities facing disturbance. This increased similarity may have effects on species at higher trophic levels, like the avifauna, by reducing trophic niches and by increasing extirpation rates via intensified species–specific interactions . Coastal wetlands need constant monitoring and management based on a comprehensive ecosystem approach that links the correct management of the physical-chemical characteristics for the maintenance of community specialization up to food web integrity.The study area is a hyperhaline coastal habitat, the Tarquinia Saltworks, located along the Tyrrhenian coasts of northern Latium in central Italy . Despite the saltworks being an artificial ecosystem, they are recognised as wetland areas according to the Ramsar Convention Bureau. Nearly http://www.unitus.it/life). The habitat was heavily impacted by this action involving bottom handling and high water flow for about one year. During the subsequent years, the lack of maintenance progressively started to drive the system toward a new state of alteration in the hydrological and trophic conditions.The long term ecological monitoring of the Tarquinia Saltworks provided a unique opportunity for testing the influence of recent important environmental changes on the local resident communities and species. The salt production was halted in 1997 with a consequent reduction of the water flow and an increase in organic and inorganic matter sedimentation resulting in several episodes of eutrophication starting with an algal bloom in 2003. During 2 and 8 cm depth) and sieved with a 0.5 mm mesh size sieve. The samples were stored in formalin solution  to preserve their integrity for subsequent ex-situ analyses, which involved filtering them on a 1 mm mesh-size funnel-shaped sieve. Sorted macroinvertebrates were then identified to the lowest taxonomic level using a dissection microscope. Further details on the sampling strategy can be found elsewhere[We analyzed three sampling sites where long-term information about the main chemical–physical parameters and the abundance of macroinvertebrates have been recorded. Benthic communities in each basin were sampled twice a year (a mid-winter and a July-summer sampling) over fourteen years (1997-2010) for an overall number of 28 samples. At the same time the values of salinity, dissolved oxygen concentration, pH, and temperature were recorded. Quantitative sampling was carried out with a Van Veen Grab ; the second period was characterized by eutrophication and started in 2003 in coincidence with the first algal bloom ; the third period started immediately after the recovery works of the LIFE02NAT/IT/8523 . We defined the halt and eutrophication periods as the pre-recovery period.The hydrological isolation/connectivity between the basins within the study area gave rise to a patchy geographic pattern in the variability of the environmental parameters, in particular, salinity and dissolved oxygen, which cn-dimensional hypervolume, sensu Hutchinson[Although ecological specialization is one of the main concepts in ecology and conservation, the numerous existing definitions and metrics require an explicit statement for applied purposes. The degtchinson). This itchinson, and thetchinson for an etchinson,31,32. Atchinson. TherefoF ratios and p-values generated by permuting the resemblance measures of actual data. Therefore, it is less sensitive to assumptions of parametric tests that are frequently violated by community data sets[We used permutational multivariate analysis of variance (PERMANOVA), with the first axis of PCA (see above) as fixed factor, to test for differences in the composition of macroinvertebrate communities along the environmental gradient throughout temporal sequences. PERMANOVA is a semi-parametric group difference test analogous to multivariate analysis of variance, but with pseudo-ata sets.p-value of significance was tested by performing 999 permutations across separated sets of data  within each group (i.e. time periods). We used the function 'adonis’ , implemented in the R package 'vegan’[We used the Bray-Curtis coefficient to construct resemblance matrices based on the abundance of sampled macroinvertebrates  and the calculated specialization index. The  'vegan’ for partNon-metric multidimensional scaling (nMDS) was used to highlight spatial and temporal patterns of community structure based on both the log-transformed abundances and specialization of sampled macroinvertebrates. A stress value ranging from 0 to 1.0 was used to measure the reliability of the ordination with zero indicating a perfect fit and all rank orders correctly represented by the relative distance between all pairs of points in the graph and with values > 0.3 indicating an arbitrary placement of the points in the graph.The authors declare that they have no competing interests.All the authors contributed to this long-term study and were involved at different times. RC, GN, and DA have been working on the environmental monitoring and ecological recovery of the Tarquinia saltworks since 1997. RC, BB, and GN contributed to the conceptual development of the work. BB and RC drafted the manuscript and BB performed the statistical analyses with CC and FC. DA and FC checked and analyzed the physical-chemical data and the macroinvertebrate list. DA, FC, GN, and CC revised the drafted manuscript. All the authors read and approved the final version of the manuscript.


Sensitivity analyses refer to investigations of the degree to which the results of a meta-analysis remain stable when conditions of the data or the analysis change. To the extent that results remain stable, one can refer to them as robust. Sensitivity analyses are rarely conducted in the organizational science literature. Despite conscientiousness being a valued predictor in employment selection, sensitivity analyses have not been conducted with respect to meta-analytic estimates of the correlation  between conscientiousness and job performance.To address this deficiency, we reanalyzed the largest collection of conscientiousness validity data in the personnel selection literature and conducted a variety of sensitivity analyses.Publication bias analyses demonstrated that the validity of conscientiousness is moderately overestimated . The misestimation of the validity appears to be due primarily to suppression of small effects sizes in the journal literature. These inflated validity estimates result in an overestimate of the dollar utility of personnel selection by millions of dollars and should be of considerable concern for organizations.The fields of management and applied psychology seldom conduct sensitivity analyses. Through the use of sensitivity analyses, this paper documents that the existing literature overestimates the validity of conscientiousness in the prediction of job performance. Our data show that effect sizes from journal articles are largely responsible for this overestimation. American Psychological Association  = 2,717; kcum [cumulative number of samples] = 4) with relatively large samples and increases to .13  with the addition of smaller samples. Finally the validity estimate increases to .16  with the addition of even smaller samples. This is consistent with an inference of publication bias resulting from the suppression of small magnitude correlations . These patterns, especially the one from the contour-enhanced funnel plot, are also inconsistent with the notion that the small sample bias  is the cause for the observed results ); msLowest value = lowest mean estimate from all analyses (than 40% .(DOCX)Click here for additional data file.S3 Tablemsp-uniform); msp-uniform); BRE = Baseline range estimate: the absolute range between Lowest value = lowest mean estimate from all analyses ((DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.


Every time you inhale the savory aromas of a home-cooked meal or the pungent smell of strong perfume, different spatial patterns of activity are evoked in odor-processing regions of the brain. Moreover, different odors elicit patterns of activity that evolve in different ways over time. For example, the timing of neuronal activity in a brain region called the olfactory bulb, relative to when an animal sniffs, conveys important information about odors. Yet relatively little is known about the behavioral relevance of the timing information generated by patterns of activity in the olfactory bulb.PLOS Biology, Justus V. Verhagen of the John B. Pierce Laboratory and his collaborators provide evidence that the mammalian olfactory system is capable of very high rates of transmission of transient information. Using an innovative optogenetics approach, they found that mice can precisely discriminate virtual odors associated with patterns of neuronal activity that differed by as little as 13 ms. According to the authors, the ability to rapidly and accurately recognize odors could provide a survival advantage, putting evolutionary pressure on the brain to maximize the use of odor information at the earliest stages of sensory processing.In a study published this week in Chlamydomonas reinhardtii that functions as an ion channel) in a subset of olfactory bulb neurons called mitral/tufted cells. Exposure to light opened channelrhodopsin 2, allowing ions to flow inside and excite these cells. Using a novel custom-designed light projector, the researchers projected high-resolution, sniff-triggered movies onto the olfactory bulb to activate the cells and thereby stimulate the perception of virtual odors. All of the movies consisted of the same spatial pattern of eight light spots. However, in static movies, all eight spots were projected simultaneously onto the olfactory bulb, whereas in dynamic movies, one set of four spots was presented before the second set of four spots. The mice were trained to discriminate between the virtual odors by licking a spout for a water reward in response to stimulation with dynamic movies but not in response to stimulation with static movies.To precisely control the timing of neuronal activity produced by virtual odors, Verhagen and his team used genetically engineered mice that expressed channelrhodopsin 2  Perception of Odors Linked to Precise Timing in the Olfactory System.doi:10.1371/journal.pbio.1002021


The Editorial on the Research TopicCombination Strategies in the Treatment of MelanomaThe successful treatment of melanoma was considered a significant challenge by oncologists for many years. However, this situation changed in 2011 with the approval of two novel agents, the anti-CTLA4 monoclonal antibody, ipilimumab, and the BRAF inhibitor, vemurafenib. These two drugs completely changed the management of metastatic melanoma and, for the first time, it became possible to significantly improve overall survival. More new therapies have followed, including other targeted agents  and immunotherapies . The availability of these new agents has resulted in a focus on combination strategies aimed at improving outcomes still further. Novel combinations of targeted drugs and/or immunotherapies represent the future treatment not only for melanoma but also for all solid tumors. The articles collected together in this Research Topic discuss various aspects of the use combination strategies in melanoma management.Ott et al. Clinical studies of combined immunotherapy and VEGF inhibition, e.g., ipilimumab plus bevacizumab, are ongoing and represent a potentially promising approach for cancer treatment.Inhibition of angiogenesis through the targeting of vascular endothelial growth factor (VEGF) has been used in the treatment of cancer for many years, although the mechanisms of its antitumor activity remain poorly understood. More recently, the advent of immune checkpoint inhibition  has led to a better understanding of the possible effects of immunotherapy on immune-mediated vasculopathy in the tumor, with the suggestion that the tumor vasculature may be an important interface between the tumor-directed immune response and the cancer itself. Initial studies of the relationship between angiogenesis, VEGF signaling and the immune system suggest that the combination of immune checkpoint blockade with VEGF inhibition has potential. The rationale for combined angiogenesis inhibition and immune checkpoint inhibition is reviewed by McArthur, who notes that the impact of pathway inhibition in the adjuvant setting, where there can be differences in the extent of response of micro-metastases or in the microenvironment that emerges following treatment, necessitates ongoing preclinical and clinical research into therapeutic targeting of the pathway. Combination approaches that look at simultaneous or sequential use of immunotherapeutic approaches with agents that target the RAF/MEK/ERK pathway are also a priority, with evidence suggesting that targeted therapies can sensitize tumor cells to immune attacks and improve the effector function of immune cells, but it should not divert attention away from the pathway that induces such profound oncogene addiction in melanoma patients whose tumors contain activating mutations in BRAF.The use of combined BRAF and MEK inhibition in advanced melanoma in order to overcome resistance and reduce toxicity is reviewed by Palmieri et al. summarize the known molecular mechanisms underlying intrinsic and acquired drug resistance and highlight the need for strategies that combine the most effective targeted treatments with cancer immunotherapies.New treatment strategies that target key effectors of the RAF/MEK/ERK pathway may display intrinsic or acquired resistance. Evidence suggests that inhibition of a single effector involved in melanoma pathogenesis may be ineffective in blocking tumor growth. As such, a better understanding of the multiple molecular alterations accounting for either response or resistance to treatments with targeted inhibitors may be useful in identifying which combination strategies are likely to be the most effective. In their paper, Sweetlove et al. investigated the effects of a MEK inhibitor (selumetinib)and a BRAF inhibitor (vemurafenib) alone and in combination with inhibitors of pan-PI3K (ZSTK474), pan-PI3K/mTOR (BEZ235), individual PI3K isoforms , or mTORC1/2 (KU-0063794) on nine metastatic BRAF-mutated melanoma cell lines. Selumetinib and vemurafenib potently inhibited cell proliferation in all cell lines, especially in those that expressed low levels of phosphorylated AKT (pAKT). Pan-PI3K and pan-PI3K/mTOR inhibitors also inhibited cell proliferation in all cell lines and enhanced the antitumor activity of selumetinib and vemurafenib in the majority of lines. These results suggest that the sensitivity of BRAF-mutant melanoma cells to BRAF or MEK inhibitors is at least partly mediated by activation of the PI3K pathway and can be enhanced by combined inhibition of the BRAF/MEK and PI3K/mTOR signaling pathways.Resistance to BRAF and MEK inhibitors can be mediated by activation of the PI3K pathway, providing a strong rationale for combination therapy in melanoma. Original research by Graziani and Lacal review the role of NRP-1 in melanoma aggressiveness and the evidence supporting its use as target of therapies for metastatic melanoma.Neuropilin-1 (NRP-1) is a transmembrane glycoprotein that acts as a coreceptor for various members of the VEGF family. Its ability to bind or modulate the activity of a number of other extracellular ligands has suggested involvement in a variety of physiological and pathological processes. NRP-1 is also expressed in a variety of cancers, suggesting a critical role in tumor progression. Increased levels of NRP-1 are correlated to tumor aggressiveness and are associated with poor prognosis. Ascierto et al. These include immunotherapeutic strategies that include adoptive transfer of ex vivo activated T cells, immunomodulatory monoclonal antibodies, and cancer vaccines. These focus on approaches being investigated in the treatment of melanoma, which has been transformed by immunotherapy into a potentially curable disease.An overview of the main immuno-oncology treatment strategies that, either alone or in combination, are undergoing clinical development is provided by The author confirms being the sole contributor of this work and approved it for publication.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


A 56-year-old female with a giant partially thrombosed unruptured carotid-ophthalmic aneurysm was treated with a Pipeline flow diverter. Three months after the procedure, in concomitance with the discontinuation of one of the antiplatelet medications, the patient suffered from a minor stroke and relapsing transient ischemic attacks. The angiography demonstrated the occlusion of the internal carotid artery, and a perfusion-weighted CT scan showed a condition of hypoperfusion. The patient underwent a double-barrel extraintracranial bypass. The postoperative course was uneventful and she has experienced no further ischemic events to date. There is increasing evidence that the flow diverters (FDs) are changing the classical treatment paradigm of cerebral aneurysms, from the occlusion of the sac to the reconstruction and healing of the vessel wall . The intWe describe the case of a patient who was treated with a FD for a giant internal carotid artery (ICA) aneurysm in whom an extraintracranial (EC-IC) bypass reversed a condition of ongoing cerebral ischemia caused by the FD thrombosis and consequent occlusion of the ICA.A 56-year-old female was initially admitted to the neurosurgical department because of retroorbital pain and mild visual deterioration in both eyes. The ophthalmologic examination showed a bilateral constriction of the visual field and a slight reduction in the visual acuity on the right side. A magnetic resonance of the brain and a digital subtraction angiography (DSA) disclosed a giant partially thrombosed aneurysm of the ICA on the right side . AlthougThis report describes a condition where an EC-IC bypass was performed to reverse a condition of ongoing cerebral ischemia and a risk of impending stroke related to the thrombosis of a FD and parent artery occlusion (PAO). Until now, apart from a patient who underwent open surgical bailout with STA-MCA bypass and intentional ICA sacrifice to relieve optic chiasm compression after unsuccessful treatment of a giant ICA aneurysm with a FD , no patiThe FD represents the most significant evolution of the endovascular approach for cerebral aneurysms. Although this device is undoubtedly appealing as it overcomes some of the limitations of the conventional endovascular procedures, this approach is not without drawbacks. A recent multicentric retrospective study has reported a mortality rate of 5.9% and a morbidity rate of 3.7% for a series of unruptured aneurysms . Recent Intrastent thrombosis and PAO, though not always clinically symptomatic, account for a significant part of the mortality and morbidity rates imputable to cerebral ischemia. Berge et al.  reportedIt should be pointed out that, as in our patient, FD thrombosis may happen even several months after deployment, and it may be related to the discontinuation of the antiplatelet therapy. While, on the one hand, this observation emphasises the importance of long-term treatment with antiplatelet medications, on the other hand, it suggests a possible drawback that may affect the long-term risk profile of the FDs. In particular, recent data regarding patients with myocardial infarction have shown that adherence to antiplatelet medications may change during long-term therapy and problems with compliance are not uncommon . The ongThe pathogenesis of cerebral ischemia in PAO may be thromboembolic or haemodynamic or a combination of the two. At the present time, in acute PAOs with thrombosis of vital perforating arteries or massive thromboembolic events, there are limited treatment options apart from medical therapy. A completely different condition occurs when the ischemic symptoms are, at least in part, of haemodynamic origin as in our patient. The recent COSS trial  and the In conclusion, one of the possible complications related to the use of the FDs is cerebral ischemia caused by FD thrombosis and PAO. In a subgroup of patients with PAO the cerebral ischemia may be of haemodynamic origin. It is important to promptly identify this subgroup of patients as an EC-IC bypass may prevent stroke-related neurological deterioration.