A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes
Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.
Salvado et al. (2015) A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes. PeerJ 3:e1183 https://doi.org/10.7717/peerj.1183
Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older
Introduction. Hospital readmission within 30 days of discharge is a target for health care cost savings through the medicare Value Based Purchasing initiative. Because of this focus, hospitals and health systems are investing considerable resources into the identification of patients at risk of hospital readmission and designing interventions to reduce the rate of hospital readmission. Malnutrition is a known risk factor for hospital readmission. Materials and Methods. All medical patients 65 years of age or older discharged from Memorial Medical Center from January 1, 2012 to March 31, 2012 who had a determination of serum albumin level and total lymphocyte count on hospital admission were studied retrospectively. Admission serum albumin levels and total lymphocyte counts were used to classify the nutritional status of all patients in the study. Patients with a serum albumin less than 3.5 grams/dL and/or a TLC less than 1,500 cells per mm3 were classified as having protein energy malnutrition. The primary outcome investigated in this study was hospital readmission for any reason within 30 days of discharge. Results. The study population included 1,683 hospital discharges with an average age of 79 years. The majority of the patients were female (55.9%) and had a DRG weight of 1.22 (0.68). 219 patients (13%) were readmitted within 30 days of hospital discharge. Protein energy malnutrition was common in this population. Low albumin was found in 973 (58%) patients and a low TLC was found in 1,152 (68%) patients. Low albumin and low TLC was found in 709 (42%) of patients. Kaplan–Meier analysis shows any laboratory evidence of PEM is a significant (p < 0.001) predictor of hospital readmission. Low serum albumin (p < 0.001) and TLC (p = 0.018) show similar trends. Cox proportional-hazards regression analysis showed low serum albumin (Hazard Ratio 3.27, 95% CI [2.30–4.63]) and higher DRG weight (Hazard Ratio 1.19, 95% CI [1.03–1.38]) to be significant independent predictors of hospital readmission within 30 days. Discussion. This study investigated the relationship of PEM to the rate of hospital readmission within 30 days of discharge in patients 65 years of age or older. These results indicate that laboratory markers of PEM can identify patients at risk of hospital readmission within 30 days of discharge. This risk determination is simple and identifies a potentially modifiable risk factor for readmission: protein energy malnutrition.
Robinson (2015) Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older. PeerJ 3:e1181 https://doi.org/10.7717/peerj.1181
Mammalian cycles: internally defined periods and interaction-driven amplitudes
The cause of mammalian cycles—the rise and fall of populations over a predictable period of time—has remained controversial since these patterns were first observed over a century ago. In spite of extensive work on observable mammalian cycles, the field has remained divided upon what the true cause is, with a majority of opinions attributing it to either predation or to intra-species mechanisms. Here we unite the eigenperiod hypothesis, which describes an internal, maternal effect-based mechanism to explain the cycles’ periods with a recent generalization explaining the amplitude of snowshoe hare cycles in northwestern North America based on initial predator abundance. By explaining the period and the amplitude of the cycle with separate mechanisms, a unified and consistent view of the causation of cycles is reached. Based on our suggested theory, we forecast the next snowshoe hare cycle (predicted peak in 2016) to be of extraordinarily low amplitude.
Ginzburg et al. (2015) Mammalian cycles: internally defined periods and interaction-driven amplitudes. PeerJ 3:e1180 https://doi.org/10.7717/peerj.1180
A new species of Brachycephalus (Anura: Brachycephalidae) from the Quiriri mountain range of southern Brazil
A new miniaturized toadled of the genus Brachycephalus (Anura: Brachycephalidae) is described from Serra do Quiriri in the municipality of Campo Alegre, Santa Catarina, southern Brazil. Specimens were collected from the leaf litter between from 1,263 and 1,318 m above sea level. The new species is distinguished from all its congeners by the combination of the following characters: snout–vent length 9.9–13.1 mm; skin on head and dorsum without dermal co-ossification; snout mucronate in dorsal view; dorsum rugose; general color brown, with a narrow orange vertebral stripe. The region where the new species is located is also shared with other endemic anuran species and has experienced strong anthropogenic impacts,suggesting that immediate actions should be taken to ensure their long-term preservation.
Pie et al. (2015) A new species of Brachycephalus (Anura: Brachycephalidae) from the Quiriri mountain range of southern Brazil. PeerJ 3:e1179 https://doi.org/10.7717/peerj.1179
Artificial light pollution increases nocturnal vigilance in peahens
Artificial light pollution is drastically changing the sensory environments of animals. Even though many animals are now living in these changed environments, the effect light pollution has on animal behavior is poorly understood. We investigated the effect of light pollution on nocturnal vigilance in peahens (Pavo cristatus). Captive peahens were exposed to either artificial lighting or natural lighting at night. We employed a novel method to record their vigilance behavior by attaching accelerometers to their heads and continuously monitoring their large head movements. We found that light pollution significantly increases nocturnal vigilance in peahens. Furthermore, the birds faced a trade-off between vigilance and sleep at night: peahens that were more vigilant spent less time sleeping. Given the choice, peahens preferred to roost away from high levels of artificial lighting but showed no preference for roosting without artificial lighting or with low levels of artificial lighting. Our study demonstrates that light pollution can have a substantial impact on animal behavior that can potentially result in fitness consequences.
Yorzinski et al. (2015) Artificial light pollution increases nocturnal vigilance in peahens. PeerJ 3:e1174 https://doi.org/10.7717/peerj.1174
A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications
Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high-specialized auditory system. Further, the large cranial cavities could help to reduce the weight of the cranium. Concerning the postcranial skeleton, Allodaposuchus hulki shows massive and robust vertebrae and forelimb bones, suggesting it could have a bulky body. The myological study performed on the anterior limb elements supports this interpretation. In addition, several bone and muscular features seem to point at a semi-erected position of the forelimbs during terrestrial locomotion. Taking all the above results into consideration, it seems plausible to suggest that A. hulki could conduct large incursions out of the water and have a semi-terrestrial lifestyle.
Blanco et al. (2015) A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications. PeerJ 3:e1171 https://doi.org/10.7717/peerj.1171
Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway
Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations.
Pellegrino et al. (2015) Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway. PeerJ 3:e1161 https://doi.org/10.7717/peerj.1161
Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda)
In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.
De Grave et al. (2015) Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda). PeerJ 3:e1167 https://doi.org/10.7717/peerj.1167
An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago
Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary. Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms. Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet. Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area.
Ősi et al. (2015) An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago. PeerJ 3:e1160 https://doi.org/10.7717/peerj.1160
Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)
The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.
Beirn et al. (2015) Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua). PeerJ 3:e1153 https://doi.org/10.7717/peerj.1153