Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Abundance, Species Composition, and Demographics of Continental Shelf Fish Assemblages throughout the Gulf of Mexico

We analyzed the results of the first comprehensive, systematic, fishery-independent survey of Gulf of Mexico (GoM) continental shelves using data collected from demersal longline sampling off the United States, Mexico, and Cuba. In total, 166 species were sampled from 343 longline sets during 2011–2017, which deployed 153,146 baited hooks, catching 14,938 fish. Abundance, species richness, and Shannon–Wiener diversity indices by station were highest in mid-shelf depths (~100 m), declining by about half in deeper waters. Six spatial assemblages were identified by testing the results of cluster analysis using similarity profile analysis and then plotting the geographic location of identified station clusters. A high degree of depth-related and horizontal zonation was evident for demersal fish species. Multispecies CPUE (number per 1,000 hookhours) was highest off the north-central (NC) and northwestern (NW) GoM and lower on the West Florida Shelf (WFS), Cuba (CUB), Yucatan Peninsula (YP), and southwestern (SW) GoM. Snappers and groupers were most abundant in the WFS and CUB, while elasmobranchs were the dominant taxa in the NC and NWGoM. Pelagic species were relatively rare everywhere (owing to the use of demersal longline gear), but were most dense off CUB. Species richness was highest in the NC and WFS subareas and lowest in the NW and CUB. Slopes of multispecies size spectra, which integrated mortality, recruitment, growth, and species interactions among size-groups, were shallowest in the NW and NC GoM and steepest off the WFS and YP. These results provide a basis for evaluating the relative resiliency potential of species assemblages across the continental shelves of the GoM, and thus for identifying subareas that are most vulnerable to acute and chronic perturbations from cumulative effects of fishing, climate change, pollution (including oil spills), habitat loss, and invasive species. Subject editor: Patrick J. Sullivan, Cornell University, Ithaca, New York *Corresponding author: smurawski@usf.edu Received December 26, 2017; accepted April 9, 2018 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 10:325–346, 2018
Réponses des cellules de Nicotiana tabacum à des molécules microbiennes : évènements de signalisation précoce, influence de la dynamique membranaire et flux de sucres

Dans son environnement la plante est confrontee a une variete de microorganismes benefiques, neutres et pathogenes, qui sont fortement dependants des ressources carbonees qu’elle libere dans le sol. Le transport de sucres, processus cle de la physiologie de la plante, est essentiel pour les interactions plantes-microorganismes et leur devenir. Au cours de l'evolution, les plantes ont acquis des mecanismes leur permettant de percevoir les signaux microbiens du milieu exterieur, et aboutissant a la transduction d’un signal specifique puis a des reponses biologiques adaptees (defense versus mutualisme) a la strategie du microorganisme. Ces reponses assurent la survie et le developpement des plantes. Mes travaux de these, menes avec un systeme « d’interaction » simplifie, contribuent a une meilleure comprehension des mecanismes sous-jacents au determinisme des interactions plantes-microorganismes. Ce systeme a permis d’etudier, sur des suspensions cellulaires de N. tabacum, les reponses cellulaires precoces declenchees suite a la perception de molecules microbiennes provenant de microorganismes a strategie pathogene avirulent ou a strategie mutualiste. Nous avons mesure des evenements de signalisation et des flux de sucres induits en reponse a ces molecules microbiennes. Nos resultats ont mis en evidence que les chitotetrasaccharides (CO4), secretes par les champignons mycorhiziens a arbuscules dans les stades pre-symbiotiques de l’interaction, mobilisent les memes evenements de signalisation precoce (H2O2 dependant de la proteine rbohD, Ca2+ cytosolique, activation de MAPK) que la cryptogeine, un eliciteur des reactions de defense ; mais avec des reponses differentes en terme d’intensite et de cinetique. Les CO4 et la cryptogeine ont par ailleurs montre des impacts distincts sur les flux de sucres et l’expression de transporteurs impliques. En complement nous avons montre un effet de la modification de la dynamique membranaire associee a la clathrine sur des evenements de signalisation declenches par la cryptogeine, ainsi que dans les flux entrants de sucres et l’expression de genes de transporteurs de sucres. Enfin, l’analyse in silico de l’interactome de transporteurs de sucres chez la plante modele A. thaliana, nous a permis d’apporter des connaissances supplementaires quant aux evenements de regulations des transporteurs de sucres et l’identification de proteines regulatrices putatives en interaction avec ces derniers. L’ensemble de ces travaux ouvrent la voie a de nouvelles recherches visant a elucider les mecanismes cellulaires et moleculaires impliques dans la mise en place des interactions entre plantes et microorganismes.
Historia Natural Insights on the Triturus marmoratus predation upon adult newts

Triturus marmoratus es una de las especies de triton mas grandes dentro de su genero, estando su dieta constituida por invertebrados y huevos y larvas de anfibios. A pesar de ello, de manera anecdotica se ha registrado tambien el consumo de ejemplares adultos de otras especies de tritones. En esta nota presentamos un nuevo caso de consumo de un ejemplar adulto de triton (Lissotriton boscai) por T. marmoratus y planteamos la hipotesis de que este consumo sea mas frecuente de lo que las evidencias publicadas sugieren.
Conservation and Population Recovery of Gharials (Gavialis gangeticus) in Nepal

Abstract: The remnant populations of Gharials, Gavialis gangeticus, are now confined to the large, deep rivers of northern India and Nepal. In lowland Nepal, the populations are restricted to a few stretches of the Narayani–Rapti and Karnali–Babai river systems. Periodic censuses of the wild populations have been made over the past 12 yr. Here, we present population trends of Gharials in the Narayani, Rapti, and Babai rivers based on these surveys. The results indicate that the combined numbers of adults and subadults have been gradually increasing since 2005, but the numbers of adults are low and female biased, with very few males recorded from all study sites. In 1978, Nepal established a captive breeding center in Chitwan National Park, from which captive-bred animals have been periodically released 4–7 yr after hatching, at which time the animals are about 1.5 m total length. The detection of hatchlings and subadult classes that are smaller than these released animals in the rivers indicates that there is natural recruitment. Therefore, collecting all nests for ex-situ breeding might not be the best strategy until more rigorous field assessments are completed to determine the relative contributions of captive-bred versus natural recruitment. We suggest that more effort should be channeled toward field assessments, including mapping and monitoring habitat availability, habitat management to ensure necessary environmental flows to create sand banks and deep pools, and research to better understand the ecology and behavior of Gharials in Nepal's rivers.
Expanding the computable reactome in Pseudomonas putida reveals metabolic cycles providing robustness

Genome-scale network reconstructions are organism-specific representations of metabolism and powerful tools for analyzing systemic metabolic properties. The use of reconstructions is limited by the lack of coverage of the metabolic reactome. We present an exhaustive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440, greatly expanding its computable metabolic states. The reconstruction, iJN1411, represents a significant expansion over other reconstructed bacterial metabolic networks. Computations based on the reconstruction exhibit high accuracy in predicting nutrient sources, growth rates, carbon flux distributions, and gene essentiality, thus providing a deep understanding of Pseudomonas metabolism. iJN1411 was used for: i) the assessment of the metabolic capabilities of P. putida as a species through multi-strain modeling, ii) deciphering the molecular mechanisms underlying metabolic robustness, and iii) identification of metabolic “capacitors” based on ATP-fueled metabolic cycles. This study represents the most complete and comprehensive bacterial metabolic reconstruction built to date, while providing computational and experimental evidence about how bacteria increase metabolic robustness, paving the way for engineering more robust biocatalysts and searching for drug targets in robust pathogens.
Photosynthetic and respiratory responses to thermal stress in the coral symbiont Symbiodinium

The symbiotic algae of corals, dinoflagellates of the genus Symbiodinium, exist in a harsh environment characterized by high temperatures, hyperoxia, ultraviolet radiation and irradiance. Despite these stressors, Symbiodinium is able to fix inorganic carbon with an apparently inferior Form II Rubisco and metabolically drive one of the earth's most diverse and productive ecosystems. Coral reefs are threatened by coral bleaching, a physiological response characterized by the death or expulsion of the algal symbionts, which has been increasing in frequency in recent decades. As the coral mutualism is based upon the exchange of carbon, the effects of thermal stress on the carbon concentrating mechanism and photosynthetic parameters of cultured Symbiodinium were assayed. A novel apparatus was devised to simultaneously measure dissolved inorganic carbon and O2 flux while simultaneously measuring photosynthetic electron transport via PAM fluorometry in small algal culture samples. There has been considerable debate whether the initial point of thermal damage during high temperature coral bleaching is in the photosynthetic apparatus or in the “dark reactions” of the Calvin-Benham-Bassham cycle. Surprisingly, the inorganic carbon requirement for maximal photosynthetic and electron transport rates was found to be reduced in Symbiodinium cultures at high temperatures, with no evidence to support damage to Rubisco or carbon fixation. High inorganic carbon levels were found to be photoprotective, implying that inorganic carbon supply by the host is central for stabilizing the symbiosis. The hyperoxic conditions of coral tissues in the light combined with high temperatures and ultraviolet radiation are conducive to the formation of damaging reactive oxygen species (ROS). Excessive generation and release of ROS by symbionts in warm conditions triggers the coral bleaching response. Here, a mitochondrial terminal alternative oxidase, widespread among plants, was detected by inhibitor assay and transcriptome analysis and described for the first time in Symbiodinium cultures. Acclimation to both high and low temperatures induced greater terminal alternative oxidase capacity, which likely has a role in mitigating mitochondrial ROS generation. High affinity for inorganic carbon and enhanced mitochondrial alternative oxidase activity of Symbiodinium are demonstrated mechanisms by which these algae are capable of maintaining physiological function under thermal stress. INDEX WORDS: Coral bleaching, coral reefs, inorganic carbon, alternative oxidase, photosynthesis, Symbiodinium PHOTOSYNTHETIC AND RESPIRATORY RESPONSES TO THERMAL STRESS IN THE CORAL SYMBIONT SYMBIODINIUM
Status of the Nile Crocodile Population in Pongolapoort Dam After River Impoundment

The major Nile crocodile Crocodylus niloticus populations in South Africa are threatened by pollution, habitat alteration/destruction, and poaching. This has highlighted the importance of other minor populations. The Phongola River Nile crocodile population was previously considered as unsubstantial. Consequently, we investigated the Nile crocodile population numbers and status and the effects of the impoundment of the Phongola River on this. In 2009–2010 we determined a minimum population number of 281 Nile crocodiles in Pongolapoort Dam using a combination of survey methods. The population structure was identified as having a minimum of 116 (41.3%) juveniles (<1.2 m total length), 31 (11.0%) subadults (1.2–2.5 m total length) and 134 (47.7%) adults (>2.5 m total length). At the commencement of the breeding season in August, crocodiles congregated at a major basking site where the main tributary entered the dam. Three major nesting areas were identified, two of which were located on the river inlet to the dam. We identified approximately 30 nesting females during the 2009/10 nesting season. Several nests were predated by the Nile monitor Varanus niloticus. There was a total recruitment failure of nests along the river inlet to the dam due to a flash flood of the Phongola River in January 2010. This preliminary study suggests that the Pongolapoort Dam Nile crocodile population has a relatively high potential reproductive output, although their annual successes may vary greatly because of loss of nesting sites as a result of water-level fluctuations and predation. It appears that the river impoundment has generally had a positive impact on this Nile crocodile population, although suitable nesting sites may become limited. Continued long-term monitoring of the Nile crocodile population in Pongolapoort Dam is required to determine if the impoundment continues to support a viable population.
Climbers from two rock outcrops in the semi-arid region of Brazil

This study aimed to recognize the floristic composition, the life form and the distribution of species of climbing plants occurring on 2 rock outcrops in the state of Pernambuco. Monthly botanical collections were made from February to September 2015 at Pedra do Cruzeiro (08°09′02.9′′ S, 035°45′22.3′′ W), municipality of Bezerros and Pico do Papagaio (07°49′25.7′′ S, 038°03′14.8′′ W), municipality of Triunfo. Fertile specimens were collected following the standard methodology in taxonomy. A total of 58 species were identified from the 2 areas, all widely distributed in Brazil and belonging to 20 botanical families. Apocynaceae, Convolvulaceae, Bignoniaceae, Dioscoreaceae and Fabaceae comprise 60% of all species. The predominant life form was phanerophyte (62%). As for the growth form, 67% of the climbers are herbaceous vines. The adaptation of twining was observed in 69% of species. Six new records for the state of Pernambuco were also identified. The rock outcrops studied show high species richness in relation to the found for climbers in other rock outcrops in the Brazilian Northeast Region.
Insect galls in three species of Copaifera L. (Leguminosae, Caesalpinioideae) occurring sympatrically in a Cerrado area (Bahia, Brazil)

The aim of this study was to characterize galls of three species of the Copaifera genus (C. sabulicola, C. luetzelburgii and C. depilis), which occur sympatrically in a Cerrado area from Bahia state. A total of 23 gall morphotypes were found, 9 morphotypes on C. sabulicola, 7 on C. luetzelburgii and 7 on C. depilis. Galls predominated on leaves and stems. The most abundant colours found among galls were brown and green. Regarding the period of the year, from 35,511 leaflets analysed, 16,322 were collected in the dry season and 19,189 in the rainy season. In the dry season, 1,635 leaflets having galls were observed, and the highest proportion was observed on C. luetzelburgii (16.31%). In relation to the rainy season, there is statistical difference in the incidence of leaflets with galls between C. sabulicola and C. depilis, these two species are affected differently during the rainy season. In general, most of the gall morphotypes were more abundant in the dry season. The gallers of 18 morphotypes cannot be determined, because the gall samples were collected occupied by parasitoids or without dwellers. Cecidomyiids induced galls in five morphotypes. Associated invertebrates belonging to the orders Hymenoptera, Diptera, Coleoptera and Acari were found among all gall morphotypes. The results obtained here indicate that the three species of Copaifera have an expressive number of galls, but lower than reported in the literature for C. langsdorffii, which is considered a super host.
Study of histopathological changes in white male rats experimentally infected by Toxoplasma gondii

Toxoplasma gondii is protozoan parasite infected different types of tissues of warm blooded animals and caused toxoplasmosis infection. Felidae is considered the final host while the rodent, reptiles, birds and mammals including human are the intermediate host. This study was aimed to isolate T. gondii from aborted placenta of infected women and experimentally infection of male rats and follow up the histopathological changes that produced in different organs such as brain, heart, liver and testes also we diagnosed the parasite in tissue of this organs. Thirty male rats Rattus norvegicus (aged (60-70) days averaged weight (200-250gm) used in this study, placed in clean plastic cages and fed on laboratory diet and drinking water), intra-peritoneal infected with suspension of parasite of aborted placenta which prepared by cutting, grinding, filtering and centrifuged of placenta sample. After 8 weeks of infection the rats were scarified and the organs brain, heart, liver and testes were fixed in 10% formalin for histological processing. The parasite were noticed and different histopathological changes such as presence of edema and proliferation of astrocytes in brain, while in liver the necrosis of hepatocytes and congestion of central vein and infiltration of inflammatory cells. In heart there were necrosis and infiltration of inflammatory cells. In testes there were congestion between the seminiferous tubules and inhibition of spermatogenesis and vaculation of spermatogonia. This study was recorded the possibility of isolation of T.gondii, noticed the parasite and follow up the histopathological changes in male rats.
A Phylogeny Based on the Concatenated 9 Protein-coding Gene Sequences of Mt Genomes among Three Gibbon Genera

The objective of this study was to reconstruct phylogenetic relationships of gibbons (3 genera, 11 species) deduced from complete sequenced mitochondrial genome sequences. According to conserved (C) / variable (V) sites ratio test, 9 selected protein coding genes were combined into a sequence with 9356 bases long including gaps. A resolved phylogenetic tree was obtained for the mitochondrial genome in the maximum-likelihood and maximum-parsimony analyses. In accordance with all previous morphological and molecular evidence, our results clearly supported monophyly of family Hylobatidae with predominantly strongly supported and each of the three genera with high support based on these coding genes. Among three genera, first Nomascus, next Symphalangus and at last Hylobates diverged, which identical to other previous research based on the whole mitochondrial genome. Our phylogenetic relationships of Nomascus group accord with Chan et al. (2010), only support values of a node of N. gabriellae (90%) were slight lower than Chan's result (97%). Among genus Hylobates, in our result, 6 species are involved and H. pileatus, H. lar, H. klossii, H. agilis, H. moloch and H. muelleri diverged sequentially.
The Expression of Solute carrier family members Genes in Mouse Ovarian Developments

Granulosa cells, which surround the oocyte within the ovarian follicle, play an essential role in creating conditions required for the development of oocytes and follicles. The solute carrier family (SLC) is comprised of influx transporters of steroidal hormones, various drugs, and several other substrates. The differential expression of selected DEGs was confirmed using in situ hybridization analysis. SLC23A3 and SLC39A10 were highly expressed in the ovary. The SLC39A10 gene was expressed in the primordial follicle stage, but SLC23A3 was expressed in the growing follicle stage. Contrastingly, the expression of SLC23A3 was increased in granulosa cells at the growing follicle stage. The differential expressions of SLC23A3 and SLC39A10 between the primordial and primary follicles were additionally confirmed by using follicle isolations. The gene expression profile from the present study may provide insight for future studies on the mechanism(s) involved in primordial-primary follicular transition and suggestions to promote follicular development in ovarian dysfunction.
Morphometry of three mosquito species vectors of West Nile Culiseta longiareolata Macquart 1838, Culiseta subochrea Edwards 1921 and Culiseta glaphyroptera Schiner 1864 collected at Collo (Northeast Algeria)

To identify the mosquito species competent for West Nile virus (WNV) transmission, we have proceeded to the morphometry study of three mosquito species belonging to the same genus Culiseta (Culiseta (Allotheobaldia) longiareolata Macquart 1838, Culiseta (Culiseta) subochrea Edwards 1921 and Culiseta (Culiseta) glaphyroptera Schiner 1864. These species have been harvested in the region of Collo (Northeast Algeria), which is characterized by a Mediterranean climate. Measurements of 32 structures considered important in the taxonomy of male and female adults, have been carried out. The exploitation of morphometric data of females and the statistical analysis showed significant differences concerning the width of the head, the length of the thorax, and the length of the tibia of the 3 leg, respectively. Highly significant differences were revealed in the length of the palps and the length of tarsi of the 3 leg. Very highly significant differences have been observed in the length of: pronotum; antennas; abdomen; wing; femur; tibia and tarsus of the 1 leg; femur; tibia and tarsus of 2 leg; femur and tibia of 3 leg. The width of: pronotum; antennas; palps; thorax; wing; tarsus of the 2 leg; tarsus of the 3 leg. For males, the statistical analysis indicated significant differences between the widths of: pronotum, femur and tarsus of the 1 leg. Highly significant differences were also noticed between the length of the abdomen and the width of the wing. Moreover, the test shows very highly significant differences concerning the length and the width of: palps; antenna; thorax; femur; tibia and tarsus of the 2 leg; tarsus of the 3 leg. The length of: pronotum; wing; femur; tibia and tarsus of the 1 leg; femur and tibia of the 3 leg. On the other hand, the study of the wing parameters showed significant differences between the length and the width of the wings and the axis (Mcu-M2), (R2-Mcu). For males, significant differences between the length of the wings and the axis (R2-Mcu) were found.
Distribution of virulence factors in Enterococcus faecalis and its adaption to conditions in the intestinal tract

Enterococcus (E.) faecalis ist Teil der normalen Intestinalflora des Menschen, kann aber auch viele Virulenzfaktoren exprimieren und schwere (nosokomiale) Infektionen hervorrufen. In dieser Arbeit wurde die Verteilung von Virulenzgenen und die Anpassung dieses Bakteriums an veranderte Umweltbedingungen auf Genom-, Proteom- und Transkriptom-Ebene untersucht. Die Virulenzfaktoren beschrankten sich nicht auf Isolate klinischer Herkunft, sondern sie waren in allen Isolaten verteilt. Proteomanalysen zeigten, dass E. faecalis sich an aerobe und anaerobe Bedingungen anpassen kann und spezifisch auf die Anwesenheit intestinaler Zellen reagiert. Die Transkriptomsequenzierung von E. faecalis aus monoassoziierten Mausen zeigte eine Anpassung der Zelloberflache und des Metabolismus sowie (Teil-) Reaktionen einer oxidativen Stressantwort.