RESUMEN

Perilla frutescens var. acuta (Lamiaceae) is widely used not only as an oil or a spice, but also as a traditional medicine to treat colds, coughs, fever, and indigestion. As an ongoing effort, luteolin-7-O-diglucuronide (1), apigenin-7-O-diglucuronide (2), and rosmarinic acid (3) isolated from P. frutescens var. acuta were investigated for their anti-adipogenic and thermogenic activities in 3T3-L1 cells. Compound 1 exhibited a strong inhibition against adipocyte differentiation by suppressing the expression of Pparg and Cebpa over 52.0% and 45.0%, respectively. Moreover, 2 inhibited the expression of those genes in a dose-dependent manner [Pparg: 41.7% (5 µM), 62.0% (10 µM), and 81.6% (50 µM); Cebpa: 13.8% (5 µM), 18.4% (10 µM), and 37.2% (50 µM)]. On the other hand, the P. frutescens var. acuta water extract showed moderate thermogenic activities. Compounds 1 and 3 also induced thermogenesis in a dose-dependent manner by stimulating the mRNA expressions of Ucp1, Pgc1a, and Prdm16. Moreover, an LC-MS/MS chromatogram of the extract was acquired using UHPLC-MS2 and it was analyzed by feature-based molecular networking (FBMN) and the Progenesis QI software (version 3.0). The chemical profiling of the extract demonstrated that flavonoids and their glycoside derivatives, including those isolated earlier as well as rosmarinic acid, are present in P. frutescens var. acuta.

Asunto(s)

Células 3T3-L1 , Fármacos Antiobesidad , Cinamatos , Depsidos , Perilla frutescens , Extractos Vegetales , Ácido Rosmarínico , Ratones , Perilla frutescens/química , Animales , Extractos Vegetales/farmacología , Extractos Vegetales/química , Depsidos/farmacología , Depsidos/química , Depsidos/aislamiento & purificación , Fármacos Antiobesidad/farmacología , Fármacos Antiobesidad/química , Fármacos Antiobesidad/aislamiento & purificación , Cinamatos/farmacología , Cinamatos/química , Cinamatos/aislamiento & purificación , Adipogénesis/efectos de los fármacos , Adipocitos/efectos de los fármacos , Adipocitos/metabolismo , Diferenciación Celular/efectos de los fármacos , Obesidad/tratamiento farmacológico , Obesidad/metabolismo , Termogénesis/efectos de los fármacos

RESUMEN

For parasites with complex multi-host life cycles, the facultative truncation of the cycle represents an adaptation to challenging conditions for transmission. However, why certain individuals are capable of abbreviating their life cycle while other conspecifics are not remains poorly understood. Here, we test whether conspecific trematodes that either follow the normal three-host life cycle or skip their final host by reproducing precociously (via progenesis) in an intermediate host differ in the composition of their microbiomes. Characterization of bacterial communities based on sequencing of the V4 hypervariable region of the 16S SSU rRNA gene revealed that the same bacterial taxa occur in both normal and progenetic individuals, independent of host identity and temporal variation. However, all bacterial phyla recorded in our study, and two-thirds of bacterial families, differed in abundance between the two morphs, with some achieving higher abundance in the normal morph and others in the progenetic morph. Although the evidence is purely correlative, our results reveal a weak association between microbiome differences and intraspecific plasticity in life cycle pathways. Advances in functional genomics and experimental microbiome manipulation will allow future tests of the significance of these findings.

Asunto(s)

Interacciones Huésped-Parásitos , Trematodos , Humanos , Animales , Estadios del Ciclo de Vida , Trematodos/genética , Adaptación Fisiológica

RESUMEN

We compared the secretion of antimicrobial peptides (AMPs) in the epidermal mucus of three healthy fish species: two aquacultured teleost species, Dicentrarchus labrax and Sparus aurata, and one wild-caught species, Pagrus pagrus. The AMPs detected in all mucus by LC-MS/MS-QTOF are: Chrysophsin-1, -2 and -3, Piscidins -1, -2, -3 and -4, terminal Histone parts and Hepcidin-like peptides. Secretion analysis of the mucus from aquacultured fish using ProGenesis IQ software distinguished the bactericidal activities of histone peptides and probiotic flora from those of other AMPs. Chrysophsin-1 was statistically the most abundant peptide in both mucus samples (p < 0.0035). A lower detection of Piscidins was also observed. Interestingly, the presence of Oncorhyncin I was most pronounced in Sparus aurata mucus. Altogether, these results suggest that Chrysophsin-1 and Oncorhyncin I are potential biomarkers for immunodetection-based studies of changes in secretion patterns which will be further investigated during bacterial challenge.

Asunto(s)

Proteoma , Dorada , Animales , Proteoma/metabolismo , Péptidos Antimicrobianos , Cromatografía Liquida/métodos , Histonas , Espectrometría de Masas en Tándem , Dorada/metabolismo , Moco/metabolismo

RESUMEN

OBJECTIVES: Urine sample manipulation including substitution, dilution, and chemical adulteration is a continuing challenge for workplace drug testing, abstinence control, and doping control laboratories. The simultaneous detection of sample manipulation and prohibited drugs within one single analytical measurement would be highly advantageous. Machine learning algorithms are able to learn from existing datasets and predict outcomes of new data, which are unknown to the model. METHODS: Authentic human urine samples were treated with pyridinium chlorochromate, potassium nitrite, hydrogen peroxide, iodine, sodium hypochlorite, and water as control. In total, 702 samples, measured with liquid chromatography coupled to quadrupole time-of-flight mass spectrometry, were used. After retention time alignment within Progenesis QI, an artificial neural network was trained with 500 samples, each featuring 33,448 values. The feature importance was analyzed with the local interpretable model-agnostic explanations approach. RESULTS: Following 10-fold cross-validation, the mean sensitivity, specificity, positive predictive value, and negative predictive value was 88.9, 92.0, 91.9, and 89.2%, respectively. A diverse test set (n=202) containing treated and untreated urine samples could be correctly classified with an accuracy of 95.4%. In addition, 14 important features and four potential biomarkers were extracted. CONCLUSIONS: With interpretable retention time aligned liquid chromatography high-resolution mass spectrometry data, a reliable machine learning model could be established that rapidly uncovers chemical urine manipulation. The incorporation of our model into routine clinical or forensic analysis allows simultaneous LC-MS analysis and sample integrity testing in one run, thus revolutionizing this field of drug testing.

Asunto(s)

Aprendizaje Automático , Preparaciones Farmacéuticas , Cromatografía Liquida , Humanos , Espectrometría de Masas , Detección de Abuso de Sustancias

RESUMEN

Despite the use of acoustic communication, many species of toads (family Bufonidae) have lost parts of the tympanic middle ear, representing at least 12 independent evolutionary occurrences of trait loss. The comparative development of the tympanic middle ear in toads is poorly understood. Here, we compared middle ear development among two pairs of closely related toad species in the genera Atelopus and Rhinella that have (eared) or lack (earless) middle ear structures. We bred toads in Peru and Ecuador, preserved developmental series from tadpoles to juveniles, and examined ontogenetic timing and volume of the otic capsule, oval window, operculum, opercularis muscle, columella (stapes), and extracolumella in three-dimensional histological reconstructions. All species had similar ontogenesis of the otic capsule, oval window, operculum, and opercularis muscle. Moreover, cell clusters of primordial columella in the oval window appeared just before metamorphosis in both eared and earless lineages. However, in earless lineages, the cell clusters either remained as small nubbins or cell buds in the location of the columella footplate within the oval window or disappeared by juvenile and adult stages. Thus, columella growth began around metamorphosis in all species but was truncated and/or degenerated after metamorphosis in earless species, leaving earless adults with morphology typical of metamorphic anurans. Shifts in the timing or expression of biochemical pathways that regulate the extension or differentiation of the columella after metamorphosis may be the developmental mechanism underlying convergent trait loss among toad lineages.

Asunto(s)

Bufonidae , Oído Medio , Animales , Bufonidae/genética , Oído , Larva , Fenotipo

RESUMEN

BACKGROUND: Species of Danionella rank among the smallest of all vertebrates and their miniature size is correlated with an extreme case of progenesis, resulting in tiny, transparent sexually mature individuals. Progenesis has affected the entire skeleton of Danionella, in which 60 skeletal elements are absent, including some of the skull roofing bones. This lack of a skull roof combined with the presence of a fully formed hearing and sound producing apparatus has led to Danionella being used as an important model for neurophysiological studies. RESULTS: Using both rank based and PGi analyses we investigate sequence heterochrony in the development of the skeleton of Danionella dracula and close relatives. Extreme heterochronic shifts affect the appearance of bony elements in Danionella dracula. This includes a delay in the appearance of most chondral skull bones, and a reduction or loss of dermal bones that would otherwise form the skull roof. In contrast, formation of the anterior region of the vertebral column, including the functionally important elements of the Weberian apparatus, is greatly accelerated. CONCLUSIONS: Here we show that the anatomical conditions that favor Danionella for brain research are the result of extreme heterochronic shifts that have acted differentially across the skeleton.

Asunto(s)

Evolución Biológica , Cyprinidae/crecimiento & desarrollo , Modelos Animales , Cráneo/crecimiento & desarrollo , Animales

RESUMEN

Tardigrades have a miniaturized body plan. Miniaturization in tardigrades is associated with the loss of several organ systems and an intermediate region of their anteroposterior (AP) axis. However, how miniaturization has affected tardigrade legs is unclear. In arthropods and in onychophorans, the leg gap genes are expressed in regionalized proximodistal (PD) patterns in the legs. Functional studies indicate that these genes regulate growth in their respective expression domains and establish PD identities, partly through mutually antagonistic regulatory interactions. Here, we investigated the expression patterns of tardigrade orthologs of the leg gap genes. Rather than being restricted to a proximal leg region, as in arthropods and onychophorans, we detected coexpression of orthologues of homothorax and extradenticle broadly across the legs of the first three trunk segments in the tardigrade Hypsibius exemplaris. We could not identify a dachshund orthologue in tardigrade genomes, a gene that is expressed in an intermediate region of developing legs in arthropods and onychophorans, suggesting that this gene was lost in the tardigrade lineage. We detected Distal-less expression broadly across all developing leg buds in H. exemplaris embryos, unlike in arthropods and onychophorans, in which it exhibits a distally restricted expression domain. The broad expression patterns of the remaining leg gap genes in H. exemplaris legs may reflect the loss of dachshund and the accompanying loss of an intermediate region of the legs in the tardigrade lineage. We propose that the loss of intermediate regions of both the AP and PD body axes contributed to miniaturization of Tardigrada.

Asunto(s)

Tamaño Corporal , Tardigrada/fisiología , Animales , Evolución Biológica , Miniaturización , Fenotipo

RESUMEN

Spermiogenesis in the progenetic spathebothriidean cestode Diplocotyle olrikii has been examined using transmission electron microscopy (TEM) for the first time. Along with the typical features of spermatozoon cytodifferentiation (e.g., the electron-dense material in the apical region of the differentiation zone in the early stage of spermiogenesis, the intercentriolar body which is composed of three electron-dense plates and two electron-lucent zones, the orthogonal development of the two flagella, a flagellar rotation, proximo-distal fusion, the presence of two pairs of electron-dense attachment zones), new for the Eucestoda is detection of the formation of two types of free flagella during spermiogenesis in progenetic D. olrikii, exhibiting either standard 9 + '1' trepaxonematan pattern, or atypical 9 + 0 structure. Various combinations of these two types of flagella resulted in the production of three types of male gametes during spermiogenesis in this spathebothriidean cestode. The first type is represented with the two axonemes of the 9 + '1' structure; the second type exhibits two different axonemes, i.e., one with 9 + '1' and the other of 9 + 0 pattern; and the third type has two axonemes with atypical 9 + 0 structure. The occurrence of three sperm types in progenetic D. olrikii is associated with typical spermiogenesis and has never been described previously in the Platyhelminthes. We suppose that heteromorphism of male gametes in D. olrikii might be linked to progenesis, i.e., the programmed sexual maturation detected during the larval/developmental stage of an organism.

Asunto(s)

Axonema/metabolismo , Cestodos/fisiología , Espermatogénesis/fisiología , Espermatozoides/citología , Animales , Flagelos/fisiología , Masculino , Microscopía Electrónica de Transmisión

RESUMEN

The life cycle of Pleurogenoides wayanadensis Shinad & Prasadan, 2018, infecting the frogs Hoplobatrachus tigerinus and Euphlyctis cyanophlyctis, is elucidated in this study. All the life cycle stages from egg to egg-producing adults were elucidated under natural conditions and successfully established in the laboratory. The life cycle took about 58 to 65 days for completion. Miracidia were released by teasing the eggs with fine needles. Sporocysts were found in the freshwater snail, Bithynia (Digoniostoma) pulchella, collected from paddy fields at Payode, Western Ghats, Wayanad region, in the months of October and November 2019. Cercariae were of the virgulate xiphidiocercous type. Metacercariae were recovered from the eyes of the damselfly naiads of the species Ischnura sp. and Copera sp., and the thorax and abdomen of the dragonfly naiads, Orthetrum sp. The metacercariae showed progenetic development. The growth and development of the metacercariae in the naiads that were exposed to cercariae, and development of the trematode in frogs that were force-fed with encysted metacercariae, have been studied at regular intervals. The prepatent period is 14-19 days. The present life cycle study of a Pleurogenoides spp. forms the seventh report from the world, fourth report from India and the third from Kerala.

Asunto(s)

Anuros/parasitología , Estadios del Ciclo de Vida , Odonata/parasitología , Caracoles/parasitología , Trematodos/crecimiento & desarrollo , Animales , India , Larva/crecimiento & desarrollo , Metacercarias/crecimiento & desarrollo , Infecciones por Trematodos/parasitología

RESUMEN

The spermatozoon ultrastructure of the progenetic cestode Diplocotyle olrikii (Spathebothriidea) has been examined using transmission electron microscopy and cytochemical staining with periodic acid-thiosemicarbazide-silver proteinate (PA-TSC-SP) for glycogen. The spermatozoon is a filiform cell, tapered at both extremities. Its moderately electron-dense cytoplasm possesses two parallel axonemes of unequal lengths. New for the Cestoda is a finding of three types of the mature spermatozoa with respect to different axonemal structure. The first type has both axonemes with standard 9 + '1' trepaxonematan pattern. The second type is represented by a spermatozoon having one axoneme with 9 + '1' structure and the second one with 9 + 0 pattern. The third type includes the two axonemes with 9 + 0 pattern. Microtubule doublets of the 9 + 0 axonemes contain either inner dynein arms or no dynein arms. In addition to the two axonemes, all three types of the mature sperm cells contain parallel nucleus, parallel cortical microtubules, four electron-dense plaques/attachment zones, and glycogen. The anterior extremity of the gamete exhibits a centriole surrounded by a semiarc of up to five electron-dense tubular structures. The distal end of the first type spermatozoa exhibits two morphological variants, represented either by (i) nucleus or (ii) remnants of the disorganized axoneme. Distal extremity of the spermatozoa of the second and third types contains doublets and singlets of disorganized axoneme. The ultrastructural characters of the spermatozoon of progenetic D. olrikii support the basal position of the Spathebothriidea within the Eucestoda.

Asunto(s)

Axonema/ultraestructura , Núcleo Celular/ultraestructura , Centriolos/ultraestructura , Cestodos/ultraestructura , Espermatozoides/ultraestructura , Animales , Citoplasma/ultraestructura , Masculino , Microscopía Electrónica de Transmisión , Espermatogénesis/fisiología

RESUMEN

BACKGROUND: Phellinus igniarius (L.) Quèl as a potential medicinal mushroom possesses multiple biological activities including hepatoprotection, but the hepatoprotective mechanism is not clear. PURPOSE: To elucidate the hepatoprotective effect and potential target of P. igniarius. METHODS: The male C57BL/6 mice were fed with the Lieber-DeCarli diet containing alcohol or isocaloric maltose dextrin as control diet with or without P. igniarius decoction (PID) in the dosage of 0.65 g/kg and 2.6 g/kg. The levels of serum biomarkers were detected by an automatic biochemistry analyser. The histopathological changes of liver were observed by hematoxylin and eosin (H&E) staining. Ultra performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (UPLC-Q/TOF-MS) was applied for investigating the dynamic changes of serum metabolites in chronic ethanol-induced liver injury mice and after treatment with PID. Ingenuity pathway analysis (IPA) was employed to identify the potential target of PID. RESULTS: PID could significantly reduce the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), triglyceride (TG) and total bile acid (TBA) in serum and improved hepatic steatosis and inflammation. In terms of metabolism, a total of 36 serum differential metabolites were identified, and PID intervention regulated 24 of them, involving the key metabolic pathways such as the biosynthesis of unsaturated fatty acids, primary bile acid biosynthesis, glycerophospholipid metabolism, fatty acids biosynthesis, ether lipid metabolism and arachidonic acid metabolism. On the mechanism, IPA showed that farnesol X receptor (FXR) was the major potential target for PID, and PID could improve chronic alcohol intake induced by the inhibition of mRNA expression of FXR in the liver and the activation of mRNA expression of FXR in the intestine in mice. CONCLUSION: The present study for the first time systematically illustrated the hepatoprotective effect of P. igniarius and preliminarily explored its potential target FXR. P. igniarius might be exploited as a promising therapeutic option for alcoholic liver injury.

Asunto(s)

Basidiomycota/química , Hepatopatías Alcohólicas/tratamiento farmacológico , Hepatopatías Alcohólicas/metabolismo , Sustancias Protectoras/farmacología , Animales , Ácido Araquidónico/metabolismo , Ácidos y Sales Biliares/metabolismo , Enfermedad Hepática Crónica Inducida por Sustancias y Drogas/tratamiento farmacológico , Enfermedad Hepática Crónica Inducida por Sustancias y Drogas/metabolismo , Enfermedad Hepática Crónica Inducida por Sustancias y Drogas/patología , Cromatografía Liquida/métodos , Etanol/toxicidad , Metabolismo de los Lípidos , Hepatopatías Alcohólicas/patología , Masculino , Espectrometría de Masas/métodos , Redes y Vías Metabólicas , Metabolómica/métodos , Ratones Endogámicos C57BL , Sustancias Protectoras/química

RESUMEN

Neophasis anarrhichae (Nicoll, 1909) Bray, 1987, unlike the majority of acanthocolpid digeneans, has an abbreviated two-host life cycle. The reproduction of rediae, development of cercariae, and their transformation into unencysted metacercariae occur within the only intermediate host, the whelk Buccinum undatum. Normally, the metacercariae develop into sexual adults (maritae) and egg production starts when the infected whelk is eaten by a wolffish Anarhichas lupus. In the White Sea, we have found three cases of infection of B. undatum by progenetic metacercariae of N. anarrichae. These metacercariae had a fully developed and functioning hermaphroditic reproductive system, and eggs were found in their uterus. Most eggs observed in the histological sections were abortive, but some contained embryos at early stages of development. The progenetic metacercariae were similar in their morphometric characteristics to the sexual adults from the wolffish, the main differences being the size of the ovary and eggs. In order to confirm progenesis, and thus a facultative one-host life cycle in N. anarrichae, we need to prove that the eggs from metacercariae are viable.

Asunto(s)

Gastrópodos/parasitología , Estadios del Ciclo de Vida , Trematodos/crecimiento & desarrollo , Animales , Cercarias , Femenino , Enfermedades de los Peces/parasitología , Genitales/anatomía & histología , Masculino , Metacercarias , Océanos y Mares , Ovario , Perciformes/parasitología , Reproducción , Trematodos/anatomía & histología

RESUMEN

Progenesis is considered to have an important role in evolution because it allows the retention of both a larval body size and shape in an adult morphology. However, the cost caused by the adoption of a progenetic process in both males and females remains to be explored to explain the success of progenesis and particularly its biased prevalence across the sexes and environments. Here, through an experimental approach, we used a facultative progenetic species, the palmate newt (Lissotriton helveticus) that can either mature at a small size and retain gills or mature after metamorphosis, to test three hypotheses for sex-specific pay-offs of progenesis in safe versus risky habitats. Goldfish were used because they caused a higher decline in progenetic than metamorphic newts. We determined that progenetic newts have a lower reproductive fitness than metamorphic newts. We also found that, when compared to metamorphs, progenetic males have lower reproductive activity than progenetic females and that predatory risk affects more progenetic than metamorphic newts. By identifying ultimate causes of the female-biased sex ratios found in nature, these results support the male escape hypothesis, that is the higher metamorphosis rate of progenetic males. They also highlight that although progenesis is advantageous in advancing the age at first reproduction, it also brings an immediate fitness cost and this, particularly, in hostile predatory environments. This means that whereas some environmental constraints could favour facultative progenesis, some others, such as predation, can ultimately counter-select progenesis. Altogether, these results improve our understanding of how developmental processes can affect the sexes differently and how species invasions can impair the success of alternative developmental phenotypes.

Asunto(s)

Evolución Biológica , Aptitud Genética , Salamandridae/crecimiento & desarrollo , Caracteres Sexuales , Maduración Sexual/genética , Animales , Tamaño Corporal , Ecosistema , Femenino , Fertilidad , Masculino , Metamorfosis Biológica , Reproducción , Salamandridae/genética , Conducta Sexual Animal

RESUMEN

Complex life cycles provide advantages to parasites (longer life span, higher fecundity, etc.), but also represent a series of unlikely events for which many adaptations have evolved (asexual multiplication, host finding mechanisms, etc.). Some parasites use a radical strategy where the definitive host is dropped; life cycle abbreviation is most often achieved through progenesis (i.e. early maturation) and reproduction in the second intermediate host. In many progenetic species, both the typical and abbreviated life cycles are maintained. However, conditions that trigger the adoption of one or the other strategy, and the pros and cons of each parasite life history strategy, are often complex and poorly understood. We used experimental infections with the trematode Coitocaecum parvum in its fish definitive host to test for potential costs of progenesis in terms of lifespan and fecundity. We show that individuals that adopt progenesis in the intermediate host are still able to establish in the definitive host and achieve higher survival and fecundity than conspecifics adopting the typical three-host life cycle. Our results and that of previous studies show that there seems to be few short-term costs associated with progenesis in C. parvum. Potential costs of self-fertilization and inbreeding are often suggested to select for the maintenance of both life-history strategies in species capable of facultative progenesis. We suggest that, at least for our focal species, there are more constraints than costs limiting its adoption. Progenesis and the abbreviated cycle may become the typical life-history strategy while reproduction in the vertebrate definitive host is now a secondary alternative when progenesis is impossible (e.g. limited host resources, etc.). Whether this pattern can be generalized to other progenetic trematodes is unknown and would require further studies.

Asunto(s)

Enfermedades de los Peces/parasitología , Reproducción , Trematodos/crecimiento & desarrollo , Infecciones por Trematodos/veterinaria , Animales , Femenino , Peces , Interacciones Huésped-Parásitos , Estadios del Ciclo de Vida , Masculino , Trematodos/genética , Trematodos/fisiología , Infecciones por Trematodos/parasitología

RESUMEN

Most Thysanoptera possess a haplo-diploid reproductive mode and reproduce via arrhenotoky. Females can mature eggs successively throughout almost their entire life, but in most terebrantian thrips spermiogenesis is complete by adult male eclosion, and testes contain only mature spermatids. In parasitoid wasps this phenomenon of preadult spermiogenesis is described as prospermatogeny. It is unclear if prospermatogeny and this predetermined sperm quantity have implications for mating strategy and fitness. In this study, we give a detailed description of mating behavior of the thripine species Echinothrips americanus, which largely corresponds with the only available data of another species of this family, Frankliniella occidentalis (Thysanoptera: Thripidae). With investigations using light microscopy, we describe for the first time the chronological sequence of internal processes during copulation. The release of male accessory gland material followed subsequently by spermatozoa indicates production of a female-determined type 1 spermatophore. Despite prospermatogeny, males are able to inseminate 10 females with an equal amount of spermatozoa. It is only the quantity of glandular material that decreases with the number of previous copulations. Based on these new findings, the reproductive strategy of this species is discussed.

Asunto(s)

Conducta Sexual Animal , Thysanoptera/fisiología , Animales , Femenino , Masculino , Reproducción

RESUMEN

Experiments involving mass spectrometry (MS)-based proteomics are widely used for analyses of connective tissues. Common examples include the use of relative quantification to identify differentially expressed peptides and proteins in cartilage and tendon. We are working on characterising so-called 'neopeptides', i.e. peptides formed due to native cleavage of proteins, for example under pathological conditions. Unlike peptides typically quantified in MS workflows due to the in vitro use of an enzyme such as trypsin, a neopeptide has at least one terminus that was not due to the use of trypsin in the workflow. The identification of neopeptides within these datasets is important in understanding disease pathology, and the development of antibodies that could be utilised as diagnostic biomarkers for diseases, such as osteoarthritis, and targets for novel treatments. Our previously described neopeptide data analysis workflow was laborious and was not amenable to robust statistical analysis, which reduced confidence in the neopeptides identified. To overcome this, we developed 'Neopeptide Analyser', a user friendly neopeptide analysis tool used in conjunction with label-free MS quantification tool Progenesis QIP for proteomics. Neopeptide Analyser filters data sourced from Progenesis QIP output to identify neopeptide sequences, as well as give the residues that are adjacent to the peptide in its corresponding protein sequence. It also produces normalised values for the neopeptide quantification values and uses these to perform statistical tests, which are also included in the output. Neopeptide Analyser is available as a Java application for Mac, Windows and Linux. The analysis features and ease of use encourages data exploration, which could aid the discovery of novel pathways in extracellular matrix degradation, the identification of potential biomarkers and as a tool to investigate matrix turnover. Neopeptide Analyser is available from https://github.com/PGB-LIV/neo-pep-tool/releases/.

RESUMEN

Miniaturization, the evolution of extremely small adult body size, is widespread amongst animals and commonly associated with novel ecological, physiological, and morphological attributes. The phenotypes of miniaturized taxa are noteworthy because they combine reductions and structural simplifications with novel traits not developed in their larger relatives. Previous research on miniature cyprinid fishes (focused predominantly on South and South East Asian taxa of a single subfamily) has identified two distinct classes of miniature taxa: proportioned dwarves and developmentally truncated miniatures. Miniaturization has also occurred independently in the subfamily Cyprininae, particularly in African lineages. We investigate the skeletal anatomy of Barboides, a genus of miniature African cyprinids that includes Africa's smallest known species of vertebrates, to assess whether miniaturization has resulted in similar organismal outcomes in different lineages of the Cyprinidae. The skeleton of Barboides is characterized by the complete absence of a number of dermal and endochondral ossifications, and marked reduction in size and/or complexity of other skeletal elements, particularly those of the dermatocranium. Absent skeletal elements in Barboides include those which develop relatively late in the ossification sequence of the non-miniature African relative 'Barbus' holotaenia suggesting that their absence in Barboides can be explained by a simple scenario of developmental truncation. In contrast to this theme of loss and reduction, the os suspensorium of Barboides is enlarged and the outer arm distally trifid and associated with a novel bulbous muscle in males. An evaluation of the skeleton of Barboides provides further evidence for a link between developmental truncation and evolutionary morphological novelty in Cyprinidae. In the spectrum of miniature cyprinids ranging from proportioned dwarves with few bones missing to highly progenetic taxa with dozens of missing bones, the two species of Barboides range roughly in the middle showing that the extremes are connected by intermediate levels of truncatedness.

Asunto(s)

Tamaño Corporal , Cyprinidae/anatomía & histología , Cyprinidae/crecimiento & desarrollo , África , Aletas de Animales/anatomía & histología , Estructuras Animales/anatomía & histología , Animales , Huesos/anatomía & histología , Región Branquial/anatomía & histología , Femenino , Masculino , Cráneo/anatomía & histología

RESUMEN

We evaluated the state of label-free discovery proteomics focusing especially on technological contributions and contributions of naturally occurring differences in protein abundance to the intersample variability in protein abundance estimates in this highly peptide-centric technology. First, the performance of popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant, and Progenesis QIP, was benchmarked using their default parameters and some modified settings. Beyond this, the intersample variability in protein abundance estimates was decomposed into variability introduced by the entire technology itself and variable protein amounts inherent to individual plants of the Arabidopsis thaliana Col-0 accession. The technical component was considerably higher than the biological intersample variability, suggesting an effect on the degree and validity of reported biological changes in protein abundance. Surprisingly, the biological variability, protein abundance estimates, and protein fold changes were recorded differently by the software used to quantify the proteins, warranting caution in the comparison of discovery proteomics results. As expected, ∼99% of the proteome was invariant in the isogenic plants in the absence of environmental factors; however, few proteins showed substantial quantitative variability. This naturally occurring variation between individual organisms can have an impact on the causality of reported protein fold changes.

Asunto(s)

Proteínas de Arabidopsis/genética , Péptidos/genética , Proteoma/genética , Proteómica/métodos , Arabidopsis/genética , Proteínas de Arabidopsis/química , Regulación de la Expresión Génica de las Plantas , Péptidos/química , Pliegue de Proteína , Proteoma/química , Programas Informáticos , Espectrometría de Masas en Tándem

RESUMEN

A number of parasites with complex life cycles can abbreviate their life cycles to increase the likelihood of reproducing. For example, some trematodes can facultatively skip the definitive host and produce viable eggs while still inside their intermediate host. The resulting shorter life cycle is clearly advantageous when transmission probabilities to the definitive hosts are low. Coitocaecum parvum can mature precociously (progenesis), and produce eggs by selfing inside its amphipod second intermediate host. Environmental factors such as definitive host density and water temperature influence the life-history strategy adopted by C. parvum in their crustacean host. However, it is also possible that information about transmission opportunities gathered earlier in the life cycle (i.e. by cercariae-producing sporocysts in the first intermediate host) could have priming effects on the adoption of one or the other life strategy. Here we document the effects of environmental parameters (host chemical cues and temperature) on cercarial production within snail hosts and parasite life-history strategy in the amphipod host. We found that environmental cues perceived early in life have limited priming effects on life-history strategies later in life and probably account for only a small part of the variation among conspecific parasites. External cues gathered at the metacercarial stage seem to largely override potential effects of the environmental conditions experienced by early stages of the parasite.

Asunto(s)

Ambiente , Estadios del Ciclo de Vida/fisiología , Trematodos/fisiología , Animales , Crustáceos/parasitología , Enfermedades de los Peces/parasitología , Peces , Interacciones Huésped-Parásitos , Humanos , Metacercarias/fisiología , Caracoles/parasitología , Infecciones por Trematodos/parasitología , Infecciones por Trematodos/veterinaria

RESUMEN

Quantification of individual proteins and even entire proteomes is an important theme in proteomics research. Quantitative proteomics is an approach to obtain quantitative information about proteins in a sample. Compared to qualitative or semi-quantitative proteomics, this approach can provide more insight into the effects of a specific stimulus, such as a change in the expression level of a protein and its posttranslational modifications, or to a panel of proposed biomarkers in a given disease state. Proteomics methodologies, along with a variety of bioinformatics approaches, are a major tool in quantitative proteomics. As the theory and technological aspects underlying the proteomics methodologies will be extensively described in Chap. 20 , and protein identification as a prerequisite of quantification has been discussed in Chap. 17 , we will focus on the quantitative proteomics bioinformatics algorithms and software tools in this chapter. Our goal is to provide researchers and newcomers a rational framework to select suitable bioinformatics tools for data analysis, interpretation, and integration in protein quantification. Before doing so, a brief overview of quantitative proteomics is provided.

Asunto(s)

Biología Computacional/métodos , Minería de Datos/métodos , Bases de Datos de Proteínas , Espectrometría de Masas/métodos , Proteínas/análisis , Proteoma , Proteómica/métodos , Algoritmos , Animales , Biomarcadores/análisis , Ensayos Analíticos de Alto Rendimiento , Humanos , Procesamiento Proteico-Postraduccional , Reproducibilidad de los Resultados , Programas Informáticos