Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans.

The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.

Genetic diversity and population structure of the rockpool shrimp Palaemon elegans based on microsatellites: evidence for a cryptic species and differentiation across the Atlantic-Mediterranean transition.

The rockpool shrimp Palaemon elegans is an ecologically important crustacean species within the European coastline fauna. In the present study, genetic diversity and population structure and connectivity were assessed by examining 21 polymorphic microsatellite loci at 13 sampling sites located along the natural distribution range. All localities showed similar levels of genetic variability. Significant deficits of heterozygosity were recorded, most likely due to the presence of null alleles. Genetic structure analyses revealed two clearly genetically distinct groups within P. elegans but without following any geographical or oceanographic basis. Thus, our results provided nuclear evidence for the existence of a Mediterranean cryptic species within P. elegans, highlighting the need to revise its taxonomic status. Regarding P. elegans sensu stricto, population structuring was reported across the Atlantic-Mediterranean transition area, where the Almería-Orán Front restricts the gene flow between the Atlantic and the Mediterranean population. Moreover, while population connectivity was suggested between all Mediterranean localities, some substructure was found within the Atlantic group. Canary Islands exhibited a weak but significant genetic differentiation from all Atlantic mainland localities, consistent with the isolation-by-distance pattern detected throughout the Atlantic population. Overall, all these findings provided new insights into the population biology of P. elegans complex.

De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes.

BACKGROUND: The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. RESULTS: A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. CONCLUSIONS: This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

Isolation and characterization of 21 polymorphic microsatellite loci for the rockpool shrimp Palaemon elegans using Illumina MiSeq sequencing.

The rockpool shrimp Palaemon elegans is considered an important crustacean species within the European coastline fauna. This species is experiencing an ongoing geographical expansion beyond its native distribution range due to unintentional human introductions. A better knowledge of the genetic diversity, geographic structure and connectivity of its populations is necessary. In the present study, microsatellite loci were isolated using the Illumina MiSeq platform. The microsatellite-enriched library sequencing produced 3.9 million raw reads. Reads were processed and primer pairs were designed for microsatellite sequences amplification. Ninety-six microsatellite loci were preliminary screened in individuals from Atlantic and Mediterranean localities. From them, 21 loci exhibited reliable polymorphism and were thoroughly characterized in 30 individuals from a Cantabrian locality (Spain). No linkage disequilibrium between pairs of loci was detected. Number of alleles per locus ranged from 2 to 12. Observed and expected heterozygosities ranged from 0.033 to 0.833 and from 0.033 to 0.869 respectively. No significant departure from the Hardy-Weinberg equilibrium was detected in most of loci. This is the first time that microsatellite markers have been developed for P. elegans. This characterized microsatellite suite provides new suitable tools for further analyses, facilitating the understanding of population genetics both in natural and introduced populations.

Cómo debemos analizar y describir la mortalidad de nuestros pacientes: experiencia del Grupo Centro Diálisis Peritoneal / How should we analyze and present mortality in our patients?: A multicentre GCDP experience

Introducción: Existen distintas estrategias para analizar la mortalidad en diálisis peritoneal (DP), con diferentes definiciones de caso, evento, tiempo en riesgo y análisis estadístico. Un método común entre los distintos registros permitiría compararlos adecuadamente y entender mejor las diferencias reales de mortalidad de nuestros pacientes. Métodos: Revisamos y describimos las estrategias de análisis de los registros autonómicos, nacional e internacionales. Incluimos análisis de supervivencia actuarial, Kaplan-Meier (KM) y riesgos-competitivos (RC). Aplicamos los diferentes enfoques a la misma base de datos (GCDP), lo que permite mostrar las diferencias aparentes con cada método. Resultados: Se incluyeron 1.890 pacientes incidentes en DP en el periodo 2003-2013 (55 años; 64,2% varones), con FRR inicial de 7ml/min; el 25% presentaba diabetes y un índice de Charlson de 3 [2-4]. Fallecieron 261 pacientes, 380 pasaron a hemodiálisis (HD) y 682 recibieron trasplante. Las tasas de mortalidad anual llegan a variar hasta un 20% en números relativos (6,4 vs. 5,2%) según el sistema aplicado. La estimación de probabilidad de mortalidad por RC es inferior a KM en todos los años: 3,6 vs. 4,0% el 1.er año; 9,0 vs. 11,9%; 15,6 vs. 28,3% y 18,5 vs. 43,3% los siguientes. Conclusiones: Aunque cada método pueda ser correcto en sí mismo y expresar diferentes enfoques, la impresión final que queda en el lector es un número que sobrestima la mortalidad. El modelo de RC expresa mejor la realidad en DP, donde el número de pacientes que pierden seguimiento (trasplante, paso a HD) cuadruplica al de los fallecidos y solo una cuarta parte continúa en DP al final del seguimiento (AU)

Introduction: There are different strategies to analyse mortality in peritoneal dialysis (PD) with different definitions for case, event, time at risk, and statistical tests. A common method for the different registries would enable proper comparison to better understand the actual differences in mortality of our patients. Methods: We review and describe the analysis strategies of regional, national and international registries. We include actuarial survival, Kaplan-Meier (KM) and competitive risk (CR) analyses. We apply different approaches to the same database (GCDP), which show apparent differences with each method. Results: A total of 1,890 incident patients in PD from 2003-2013 were included (55 years; men 64.2%), with initial RRF of 7 ml/min; 25% had diabetes and a Charlson index of 3 [2-4]; 261 patients died, 380 changed to haemodialysis (HD) and 682 received a transplant. Annual mortality rates varied up to 20% in relative numbers (6.4 vs. 5.2%) depending on the system applied. The estimated probability of mortality measured by CR progressively differs from the KM over the years: 3.6 vs. 4.0% the first year, then 9.0 vs. 11.9%, 15.6 vs. 28.3%, and 18.5 vs. 43.3% the following years. Conclusions: Although each method may be correct in themselves and express different approaches, the final impression left on the reader is a number that under/overestimates mortality. The CR model better expresses the reality of PD, where the number of patients lost to follow-up (transplant, transfer to HD) it is 4 times more than deceased patients and only a quarter remain on PD at the end of follow up (AU)

How should we analyze and present mortality in our patients?: A multicentre GCDP experience.

INTRODUCTION: There are different strategies to analyse mortality in peritoneal dialysis (PD) with different definitions for case, event, time at risk, and statistical tests. A common method for the different registries would enable proper comparison to better understand the actual differences in mortality of our patients. METHODS: We review and describe the analysis strategies of regional, national and international registries. We include actuarial survival, Kaplan-Meier (KM) and competitive risk (CR) analyses. We apply different approaches to the same database (GCDP), which show apparent differences with each method. RESULTS: A total of 1,890 incident patients in PD from 2003-2013 were included (55 years; men 64.2%), with initial RRF of 7ml/min; 25% had diabetes and a Charlson index of 3 [2-4]; 261 patients died, 380 changed to haemodialysis (HD) and 682 received a transplant. Annual mortality rates varied up to 20% in relative numbers (6.4 vs. 5.2%) depending on the system applied. The estimated probability of mortality measured by CR progressively differs from the KM over the years: 3.6 vs. 4.0% the first year, then 9.0 vs. 11.9%, 15.6 vs. 28.3%, and 18.5 vs. 43.3% the following years. CONCLUSIONS: Although each method may be correct in themselves and express different approaches, the final impression left on the reader is a number that under/overestimates mortality. The CR model better expresses the reality of PD, where the number of patients lost to follow-up (transplant, transfer to HD) it is 4 times more than deceased patients and only a quarter remain on PD at the end of follow up.

Peritoneal Dialysis Can Be an Option for Dominant Polycystic Kidney Disease: an Observational Study.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) has been considered a relative contraindication for peritoneal dialysis (PD), although there are few specific studies available. METHODS: A multicenter historical prospective matched-cohort study was conducted to describe the outcome of ADPKD patients who have chosen PD. All ADPKD patients starting PD (n = 106) between January 2003 and December 2010 and a control group (2 consecutive patients without ADPKD) were studied. Mortality, PD-technique failure, peritonitis, abdominal wall leaks and cyst infections were compared. RESULTS: Patients with ADPKD had similar age but less comorbidity at PD inclusion: Charlson comorbidity index (CCI) 4.3 (standard deviation [SD] 1.6) vs 5.3 (SD 2.5) p < 0.001, diabetes mellitus 5.7% vs 29.2%, p < 0.001 and previous cardiovascular events 10.4% vs 27.8%, p < 0.001. No differences were observed in clinical events that required transient transfer to hemodialysis, nor in peritoneal leakage episodes or delivered dialysis dose. The cyst infection rate was low (0.09 episodes per patient-year) and cyst infections were not associated to peritonitis episodes. Overall technique survival was similar in both groups. Permanent transfer to hemodialysis because of surgery or peritoneal leakage was more frequent in ADPKD. More ADPKD patients were included in the transplant waiting list (69.8 vs 58%, p = 0.04) but mean time to transplantation was similar (2.08 [1.69 - 2.47] years). The mortality rate was lower (2.5 vs 7.6 deaths/100 patient-year, p = 0.02) and the median patient survival was longer in ADPKD patients (6.04 [5.39 - 6.69] vs 5.57 [4.95 - 6.18] years, p = 0.024). CONCLUSION: Peritoneal dialysis is a suitable renal replacement therapy option for ADPKD patients.

First episodes of peritoneal infection: description and prognostic factors.

INTRODUCTION: Peritonitis is one of the most common and severe complications associated with peritoneal dialysis (PD), constituting the primary cause of catheter loss and exit from the dialysis technique. The incidence and aetiology of peritonitis episodes vary based on geographical region, and change over time. For this reason, it is vital to maintain an updated understanding of the current risk factors and prognostic factors associated with peritonitis. METHOD: We performed an observational, multi-centre, prospective cohort study with a maximum follow-up period of 7 years (2003-2010), which included 1177 patients and a total of 476 first episodes of peritonitis (total: 1091 cases of peritonitis). RESULTS: We describe the characteristics of the first episode of peritonitis from a large and current study sample. The factors associated with a shorter interval until the first episode of peritonitis as selected by the multivariate analysis included prior cardiovascular comorbidity (Hazard Ratio [HR]: 1.25 [1.04-1.58]), having previously received haemodialysis (HR: 1.39 [1.10-1.76]) or a kidney transplant (HR: 1.38 [1.10-1.93]), having started PD on a manual modality (HR: 1.39 [1.13-1.73]), and initial age >70 years (HR: 1.53 [1.23-1.90]). The first episode of peritonitis was associated with a 7.8% rate of recurrence, an 11.7% rate of catheter removal, and a mortality rate within one month of the episode of 1.3%. The progression of peritonitis infections depended on the type of causal microorganism. We calculated a greater risk for gram-negative bacterial infections (Odds Ratio [OR]: 5.31 [2.26-12.48]) and the aggregate group of infections caused by multiple microorganisms, fungal infections, and mycobacterial infections (OR: 38.24 [13.84-105.63]), as compared to gram-positive bacterial infections. CONCLUSION: The development of a first case of peritonitis depends on the characteristics of the patient upon starting dialysis, comorbidities present, and the technique used. Patients at a greater risk for peritonitis must receive special care during training and follow-up.

Liquen amiloide / Lichen amyloidosis

El liquen amiloide es una forma de amiloidosis cutánea primaria, papular, intensamente pruriginosa, de etiología desconocida. La biopsia muestra depósitos de amiloide limitados a la dermis papilar, que producen birrefringencia verdosa con la tinción de rojo Congo. Presentamos el caso de una paciente con un cuadro clínico e histológico típico, y efectuamos una revisión de la literatura

Liquen amiloide / Lichen amyloidosis

El liquen amiloide es una forma de amiloidosis cutánea primaria, papular, intensamente pruriginosa, de etiología desconocida. La biopsia muestra depósitos de amiloide limitados a la dermis papilar, que producen birrefringencia verdosa con la tinción de rojo Congo. Presentamos el caso de una paciente con un cuadro clínico e histológico típico, y efectuamos una revisión de la literatura (AU)