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opencc-by-4.0Nov 2020View details →

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks

Matlab output files and raw data used for the evaluation presented in "DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks" <a href="https://github.com/MetExplore/dexom">https://github.com/MetExplore/dexom</a>

opencc-by-4.0Dec 2019View details →

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon

Supplementary Information for the manuscript: "DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon"

opencc-zeroNov 2020View details →

Tactic-specific antimicrobial activity suggests a parental care function for accessory glands in a marine toadfish

Males of some species possess extra reproductive organs called accessory glands which are outgrowths of the testes or sperm duct. These organs have a well-established role in reproduction; however, they also appear to have other important functions that are less understood. Here we investigate the function of the highly complex accessory glands of a marine toadfish, Porichthys notatus, a fish with two reproductive male types: large care-providing 'guarder' males and small non-caring 'sneaker' males. While both male types have accessory glands, guarder male accessory glands are much larger relative to their body size. We show that accessory gland fluids strongly inhibit the growth of bacterial genera associated with unhealthy eggs and have no effect on the growth of strains isolated from healthy eggs. This antibacterial effect was particularly pronounced for extracts from guarder males. Furthermore, we demonstrate that both healthy and unhealthy plainfin midshipman eggs have diverse but distinct microbial communities that differ in their composition and abundance. The highly specific inhibitory capacity of accessory gland fluid on bacteria from unhealthy eggs was robust across a wide range of ecologically relevant temperatures and salinities. Collectively, these ecological and molecular observations suggest a care function for the accessory gland, mediated by antimicrobial agents.

opencc-zeroDec 2020View details →

Prostate-specific deletion of Cdh1 induces murine prostatic inflammation and bladder overactivity

Benign Prostatic Hyperplasia (BPH) is an age-related debilitating prostatic disease that is frequently associated with prostatic inflammation and bothersome lower urinary tract symptoms (LUTS). Animal models have shown that formalin- and bacterial-induced prostatic inflammation can induce bladder dysfunction; however, the underlying mechanisms contributing to prostatic inflammation in BPH and bladder dysfunction are not clear. We previously reported that E-cadherin expression in BPH is down-regulated in hyperplastic nodules compared to expression in adjacent normal tissues. Here, we explored the potential consequences of prostatic E-cadherin down-regulation on the prostate and bladder in vivo using an inducible murine model of prostate luminal epithelial-specific deletion of Cdh1. The PSA-CreERT2 transgenic mouse strain expressing tamoxifen-inducible CreERT2 recombinase driven by a 6-kb human PSA promoter/enhancer was crossed with the B6.129-Cdh1tm2Kem/J mouse to generate bigenic PSA-CreERT2/Cdh1-/- mice. Deletion of E-cadherin was induced by transient administration of tamoxifen when mice reached sexual maturity (7 weeks of age). At 21-23 weeks of age, the prostate, bladder, and prostatic urethra were examined histologically, and bladder function was assessed using Void Spot Assays and cystometry. Mice with Cdh1 deletion had increased prostatic epithelial hyperplasia, inflammation, and stromal changes at 21-23 weeks of age, as well as changes in bladder voiding function compared to age-matched controls. Thus, loss of E-cadherin in the murine prostate could result in prostatic defects that are characteristic of BPH and lower urinary tract symptoms, suggesting that E-cadherin down-regulation could be a driving force in human BPH development and progression.

opencc-zeroDec 2020View details →

Data from: Inter- and intra-specific variation of spider mite susceptibility to fungal infections: implications for the long-term success of biological control

Spider mites are severe pests of several annual and perennial crops worldwide, often causing important economic damages. As rapid evolution of pesticide resistance in this group hampers the efficiency of chemical control, alternative control strategies, such as the use of entomopathogenic fungi, are being developed. However, while several studies have focused on the evaluation of the control potential of different fungal species and/or isolates as well as their compatibility with other control methods (e.g. predators or chemical pesticides), knowledge on the extent of inter- and intraspecific variation in spider mite susceptibility to fungal infection is as yet incipient. Here, we measured the mortality induced by two generalist fungi, Beauveria bassiana and Metarhizium brunneum, in 12 spider mite populations belonging to different Tetranychus species: T. evansi, T. ludeni, the green form of T. urticae and the red form of T. urticae, within a full factorial experiment. We found that spider mite species differed in their susceptibility to infection by both fungal species. Moreover, we also found important intraspecific variation for this trait. These results draw caution on the development of single strains as biocontrol agents. Indeed, the high level of intraspecific variation suggests that (a) the one-size-fits-all strategy may fail to control spider-mite populations and (b) hosts resistance to infection may evolve at a rapid pace. Finally, we propose future directions to better understand this system and improve the long-term success of spider mite control strategies based on entomopathogenic fungi.

opencc-by-4.0Dec 2020View details →

Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses

Transposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in twenty-six genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The twenty-six genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.

opencc-zeroApr 2020View details →

Distinct DNA methylation signatures in neuroendocrine tumors specific for primary site and inherited predisposition

Purpose: To compare the deoxyribonucleic acid (DNA) methylation signature of neuroendocrine tumors (NETs) by primary tumor site and inherited predisposition syndromes von Hippel–Lindau disease (VHL) and multiple endocrine neoplasia type 1 (MEN1). Methods Genome-wide DNA methylation (835 424 CpGs) of 96 NET samples. Principal components analysis (PCA) and unsupervised hierarchical clustering analyses were used to determine DNA methylome signatures. Results: Hypomethylated CpGs were significantly more common in VHL-related versus sporadic and MEN1-related NETs (P &lt; .001 for both comparisons). Small-intestinal NETs (SINETs) had the most differentially methylated CpGs, either hyper- or hypomethylated, followed by duodenal NETs (DNETs) and pancreatic NETs (PNETs, P &lt; .001 for all comparisons). There was complete separation of SINETs on PCA, and 3 NETs of unknown origin clustered with the SINET samples. Sporadic, VHL-related, and MEN1-related PNETs formed distinct groups on PCA, and VHL clustered separately, showing pronounced DNA hypomethylation, while sporadic and MEN1-related NETs clustered together. MEN1-related PNETs, DNETs, and gastric NETs each had a distinct DNA methylome signature, with complete separation by PCA and unsupervised clustering. Finally, we identified 12 hypermethylated CpGs in the 1A promoter of the APC (adenomatous polyposis coli) gene, with higher methylation levels in MEN1-related NETs versus VHL-related and sporadic NETs (P &lt; .001 for both comparisons). Conclusions: DNA CpG methylation profiles are unique in different primary NET types even when occurring in MEN1-related NETs. This tumor DNA methylome signature may be utilized for noninvasive molecular characterization of NETs, through DNA methylation profiling of biopsy samples or even circulating tumor DNA in the near future.

opencc-zeroDec 2019View details →

Fungal root-endophytes influence plants in a species-specific manner that depends on plant's growth stage

The mycobiome (fungal microbiome) influences plants— from seed germination to full maturation. While many studies on fungal-plant interaction studies have focused on known mutualistic and pathogenic fungi, the functional role of ubiquitous endophytic fungi remains little explored. We examined how root-inhabiting fungi (endophytes) influence range expanding plant species. We isolated endophytes from three European intra-continental range-expanders and three congenerics that are native both in the range-expander's original (southern Europe) and new (northern Europe) range. To standardize our collection, endophytes were obtained from all six plant species growing under controlled conditions in northern (new range of the range-expander) and southern (native range of the range-expander) soils. We cultivated, molecularly identified and tested the effects of all isolates on seed germination, and growth of seedlings and older plants. Most of the 34 isolates could not be functionally characterized based on their taxonomic identity and literature information on functions. Endophytes affected plant growth in a plant species-endophyte specific manner, but overall differed between range-expanders and natives. While endophytes reduced germination and growth of range-expanders compared to natives, they reduced seedling growth of natives more than of range-expanders. Synthesis: We conclude that endophytic fungi have a direct effect on plant growth in a plant growth stage-dependent manner. While these effects differed between range expanders and natives, the effect strength and significance varied among the plant genera included in the present study. Nevertheless, endophytes likely influence establishment of newly arriving plants and influence vegetation dynamics

opencc-zeroDec 2020View details →

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

In fishes, swimming performance is considered an important metric to measure fitness, dispersal, and migratory abilities. Swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g., connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water quality parameters and flow velocity. In this study, we automated the control of multi-lane swimming chambers for small fishes by developing an open-source algorithm. This automation allowed us to execute repeatable flow scenarios and reduce operator interference and inaccuracies in flow velocity typically associated with manual control. Furthermore, we made structural modifications to a prior design to reduce areas of lower flow velocity. We then validated the flow dynamics of the new chambers using computational fluid dynamics and particle tracking software. The algorithm provided accurate alignment between set and measured flow velocities and we used it to test whether faster critical swimming speed (Ucrit) protocols (i.e., shorter time intervals and higher velocity increments) would increase Ucrit of early life stages of two tropical fish species (4-10 mm standard length). The Ucrit of barramundi (Lates calcarifer) and cinnamon anemonefish (Amphiprion melanopus) increased linearly with fish length, but in cinnamon anemonefish, Ucrit started to decrease upon metamorphosis. Swimming protocols using longer time intervals (>2.5 times increase) negatively affected Ucrit in cinnamon anemonefish but not in barramundi. These species-specific differences in swimming performance highlight the importance of testing suitable Ucrit protocols prior to experimentation. Automated control of flow velocity will create more accurate and repeatable data on swimming performance of larval fishes. Integrating refined measurements into individual-based models will support future research on the effects of environmental change.

PLATE 9 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 9. Male genitalia (without aedeagus) in dorsal projection and tegumens of M. distans stat. n. (1, 2, 7, 8), M. alatauica (3, 9, 10) and M. aurelia (4–6, 11–14) from different localities: 1, 2, 7, 8—Tian–Shan, the Bajankol river; 3, 9—Burchansarytau; 10—Dzhungarian Alatau, the Koksu river; 4—Chelyabinsk Region, Arkaim; 5—Omsk Region, Kalachinsk; 6, 14—Novosibirsk Region, Karasuk Distr.; 11—Moscow Region, Lukhovitsy Distr.; 12—Crimea, Chatyr–Dah; 13– Vinnitsa Region, Mohyliv–Podilskyi Distr.

PLATE 6 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 6. Photos of M. alatauica from different localities of Dzhungarian Alatau Mts.: 1–4 males, upperside; 5–8—females, upperside; 9–12—males, underside; 13–16—females, underside; 1, 4, 8, 9, 12, 16—the Tentek river; 2, 3, 5, 6, 10, 11, 13, 14—Burchansarytau, the Usek river; 7, 15—the Tyshkan Mts.

PLATE 2 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 2. Phylogenetic tree showing the relationship between species of the genus Mellicta according to the analysis of 658 bp the COI gene fragment. A phylogenetic tree was constructed using the Bayesian analysis (BA) and the Maximum Likelihood (ML) methods. The nodes are marked with Bayesian posterior probabilities (PP) and bootstrap (BS). Aglais io and Nymphalis antiopa used as outgroups.

PLATE 5 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 5. Photos of M. aurelia from different localities: 1–8 males, upperside; 9–12—females, upperside; 13–20—males, underside; 21–24—females, underside; 1, 13—Crimea, Chatyr–Dah; 2, 14—Vinnitsa Region., Mohyliv–Podilskyi Distr.; 3, 15—Moscow Region, Yegoryevsk Distr.; 4, 16—Republic of Bashkortostan, Uchaly Distr.; 5, 17—Orenburg Region, Buzuluk; 6, 18—Volgograd Region, Kamyshyn Distr.; 7, 19—Chelyabinsk Region, Arkaim; 8, 20—Novosibirsk Region, Karasuk Distr.; 9, 21—Crimea, Sudak, Lesnoe Vill.; 10, 22—Orenburg Region, Kuvandyk; 11, 23—Chelyabinsk Region, Chebarkul; 12, 24—Novosibirsk Region, Karasuk Distr.

PLATE 10 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 10. Female genitalia (without the anal papillae, copulatory bursa, and anterior and posterior apophyses) of M. distans stat. n. (1–3) and M. alatauica (4–6) from different localities: 1–3—Tian–Shan, the Bajankol river; 4—Burchansarytau; 5—Kulja; 6—Dzhungarian Alatau, the Kora river. The red arrow points a short postvaginal plate. The blue arrow points rounded side lobes, protruding sideways. The green arrow points an enlarged antrum.

PLATE 1 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 1. Distribution of M. distans stat. n., M. alatauica, M. aurelia and M. menetriesi in Kazakhstan and adjacent territories.

PLATE 8 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 8. Structures of male genitalia (a—valva, b—aedeagus) of M. aurelia from different localities: 1—Moscow Region, Lukhovitsy Distr.; 2—Crimea, Chatyr–Dah; 3—Vinnitsa Region, Mohyliv–Podilskyi Distr.; 4—Republic of Bashkortostan, Uchaly Distr.; 5—Orenburg Region, Buzuluk; 6—Volgograd Region, Kamyshyn Distr.; 7—Chelyabinsk Region, Chebarkul; 8—Chelyabinsk Region, Arkaim; 9—Novosibirsk Region, Karasuk Distr. The red arrow points a down–curved caudal process of the valva. The blue arrow points a straight and is directed upwards vesica.

PLATE 11 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 11. Female genitalia (without the anal papillae, copulatory bursa, and anterior and posterior apophyses) of M. aurelia from different localities: 1, 2—Crimea, Ai–Petri; 3—Vinnitsa Region, Mohyliv–Podilskyi Distr.; 4—Republic of Bashkortostan, Uchaly Distr.; 5—Novosibirsk Region, Karasuk Distr.; 6—Chelyabinsk Region, Chebarkul. The red arrow points a short postvaginal plate.

PLATE 4 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 4. Photos of M. distans stat. n. from Tian–Shan: 1–16—E. edge of Terskei Alatau, the Bajankol river (1–4—males, upperside; 5–8—females, upperside; 9–12—males, underside; 13–16—females, underside); 17, 18—Holotype, male, the Tekkes river, Trustees Natural History Museum, used with permission. Photo A. Devyatkin.

PLATE 7 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters

PLATE 7. Structures of male genitalia (a—valva, b—aedeagus) of M. distans stat. n. (1–6) and M. alatauica (7–9) from different localities: 1–6—Tian–Shan, the Bajankol river; 7—Dzhungarian Alatau, the Koksu river; 8, 9—Burchansarytau. The red arrow points to a down–curved caudal process of the valva. The blue arrow points a curved and directed downwards vesica.