Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.

The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.

Taxonomical and functional diversity dynamics of conspicuous echinoderms in the northeastern tropical Pacific over a decade.

Understanding what determines spatio-temporal changes in echinoderm assemblages from an integrative perspective that considers biodiversity, species evenness, and species' niches could permit superior community-scale characterizations of habitat resilience to disturbance. Such an approach was taken herein by tracking a Central Mexican Pacific echinoderm assemblage between 2012 and 2021, and higher richness, diversity, evenness, and functional entity counts were associated with more heterogeneous benthic assemblages. Echinoderm taxonomic composition was influenced by ENSO events, with higher functional diversity found during La Niña events. Conservation strategies should focus on species with unique functional traits to maintain the balance of coral community functionality.

Chilensosides E, F, and G-New Tetrasulfated Triterpene Glycosides from the Sea Cucumber Paracaudina chilensis (Caudinidae, Molpadida): Structures, Activity, and Biogenesis.

Three new tetrasulfated triterpene glycosides, chilensosides E (1), F (2), and G (3), have been isolated from the Far-Eastern sea cucumber Paracaudina chilensis (Caudinidae, Molpadida). The structures were established based on extensive analysis of 1D and 2D NMR spectra and confirmed by HR-ESI-MS data. The compounds differ in their carbohydrate chains, namely in the number of monosaccharide residues (five or six) and in the positions of sulfate groups. Chilensosides E (1) and F (2) are tetrasulfated pentaosides with the position of one of the sulfate groups at C-3 Glc3, and chilensoside G (3) is a tetrasulfated hexaoside. The biogenetic analysis of the glycosides of P. chilensis has revealed that the structures form a network due to the attachment of sulfate groups to almost all possible positions. The upper semi-chain is sulfated earlier in the biosynthetic process than the lower one. Noticeably, the presence of a sulfate group at C-3 Glc3-a terminal monosaccharide residue in the bottom semi-chain of compounds 1 and 2-excludes the possibility of this sugar chain's further elongation. Presumably, the processes of glycosylation and sulfation are concurrent biosynthetic stages. They can be shifted in time in relation to each other, which is a characteristic feature of the mosaic type of biosynthesis. The hemolytic action of compounds 1-3 against human erythrocytes and cytotoxic activities against five human cancer cell lines were tested. The compounds showed moderate hemolytic activity but were inactive against cancer cells, probably because of their structural peculiarities, such as the combination of positions of four sulfate groups.

Characterization and Expression of Holothurian Wnt Signaling Genes during Adult Intestinal Organogenesis.

Wnt signaling has been shown to play multiple roles in regenerative processes, one of the most widely studied of which is the regeneration of the intestinal luminal epithelia. Most studies in this area have focused on self-renewal of the luminal stem cells; however, Wnt signaling may also have more dynamic functions, such as facilitating intestinal organogenesis. To explore this possibility, we employed the sea cucumber Holothuria glaberrima that can regenerate a full intestine over the course of 21 days after evisceration. We collected RNA-seq data from various intestinal tissues and regeneration stages and used these data to define the Wnt genes present in H. glaberrima and the differential gene expression (DGE) patterns during the regenerative process. Twelve Wnt genes were found, and their presence was confirmed in the draft genome of H. glaberrima. The expressions of additional Wnt-associated genes, such as Frizzled and Disheveled, as well as genes from the Wnt/ß-catenin and Wnt/Planar Cell Polarity (PCP) pathways, were also analyzed. DGE showed unique distributions of Wnt in early- and late-stage intestinal regenerates, consistent with the Wnt/ß-catenin pathway being upregulated during early-stages and the Wnt/PCP pathway being upregulated during late-stages. Our results demonstrate the diversity of Wnt signaling during intestinal regeneration, highlighting possible roles in adult organogenesis.

Genetic differentiation of five sea cucumber species from the Red Sea, Hurghada, Egypt / Diferenciação genética de cinco espécies de pepino-do-mar do Mar Vermelho, Hurghada, Egito

This study aimed to assess the genetic differentiation and relationship among five sea cucumber species from the Red Sea in Egypt, namely Holothuria atra, H. impatiens, H. leucospilota, Actinopyga crassa and A. mauritiana, using Inter Simple Sequence Repeated (ISSR) and Start Codon Targeted (SCoT) markers. A collection of 100 specimens, with 20 individuals per species, was gathered for the analysis. With ten ISSR primers, 135 amplified bands were detected, including 11 distinct species-specific bands, indicating high-level polymorphism among species. Using ten SCoT primers, 151 amplicons were generated, including 30 species-specific bands, with 52% polymorphic bands indicating high-level polymorphism among species. The degree of genetic similarity (GS) among the different genotypes of species was calculated based on ISSR bands analysis, which ranged from 93% between H. atra and H. impatiens to 86% between H. atra and A. crassa. The highest genetic similarity was observed between H. atra and H. impatiens (90%), while the lowest was identified between A. crassa and A. mauritiana (75%) using SCoT bands. Notably, the ISSR and SCoT-based DNA analysis revealed similar genetic relationships between H. atra and H. impatiens compared to other sea cucumber species studied. This study provides new insights into the genetic diversity and relationship among sea cucumber species in the Red Sea, which could have implications for their conservation and management.

Este estudo teve como objetivo avaliar a diferenciação genética e a relação entre cinco espécies de pepinos-do-mar do Mar Vermelho no Egito, quais sejam, Holothuria atra, Holothuria impatiens, Holothuria leucospilota, Actinopyga crassa e Actinopyga mauritiana, usando marcadores Inter Simple Sequence Repeated (ISSR) e Start Codon Targeted (SCoT). Uma coleção de 100 espécimes, com 20 indivíduos por espécie, foi reunida para análise. Com 10 primers ISSR, 135 bandas amplificadas foram detectadas, incluindo 11 bandas específicas de espécies distintas, indicando polimorfismo de alto nível entre as espécies. Usando 10 primers SCoT, 151 amplicons foram gerados, incluindo 30 bandas específicas da espécie, com 52% de bandas polimórficas indicando polimorfismo de alto nível entre as espécies. O grau de similaridade genética (GS) entre os diferentes genótipos das espécies foi calculado com base na análise das bandas ISSR, que variou de 93% entre H. atra e H. impatiens a 86% entre H. atra e A. crassa. A maior similaridade genética foi observada entre H. atra e H. impatiens (90%), enquanto a menor foi identificada entre A. crassa e A. mauritiana (75%) usando bandas SCoT. Notavelmente, a análise de DNA baseada em ISSR e SCoT revelou relações genéticas semelhantes entre H. atra e H. impatiens em comparação com outras espécies de pepino-do-mar estudadas. Este estudo fornece novas informações sobre a diversidade genética e a relação entre as espécies de pepino-do-mar no Mar Vermelho, o que pode ter implicações para sua conservação e manejo.

Phytotoxicity of organic extracts of five medicinal plants of the Neotropical savanna / Fitotoxicidade de extratos orgânicos de cinco plantas medicinais do Cerrado

Medicinal plants produce a high diversity of secondary metabolites with different biological activities, which are commonly evaluated when prospecting for bioherbicides. We analyzed the phytotoxic activity of organic extracts from the leaves of five medicinal species, Byrsonima intermedia, Moquiniastrum polymorphum, Luehea candicans, Miconia chamissois, and Qualea cordata. Phytotoxicity was evaluated on the initial growth of cucumber seedlings through tests with different concentrations of hexane, ethyl acetate, and methanol extracts. The results showed that all organic extracts and all concentrations affected cucumber development, with methanol extracts generally showing the greatest negative effect on the initial growth of the target species. The only exception was for M. chamissois extracts, in which the hexane extract had the greatest phytotoxicity. Furthermore, the organic extracts were subjected to preliminary phytochemical analysis, revealing the widespread presence of alkaloids along with other chemical classes. All the study species are thus potential candidates for use as natural herbicides.

As plantas medicinais são comumente avaliadas na prospecção de bioherbicidas, por produzirem uma alta diversidade de metabólitos secundários com diferentes atividades biológicas. Analisamos a atividade fitotóxica de extratos orgânicos de folhas de cinco espécies medicinais, Byrsonima intermedia, Moquiniastrum polymorphum, Luehea candicans, Miconia chamissois e Qualea cordata. A fitotoxicidade foi avaliada no crescimento inicial de plântulas de pepino por meio de testes com diferentes concentrações de extratos de hexano, acetato de etila e metanol. Os resultados mostraram que todos os extratos orgânicos e todas as concentrações afetaram o desenvolvimento de pepino, com os extratos metanólicos geralmente apresentando a maior inibição no crescimento inicial da espécie-alvo. A única exceção foram os extratos de M. chamissois, em que o extrato hexânico apresentou a maior fitotoxicidade. Adicionalmente, os extratos orgânicos foram submetidos a análises fitoquímicas preliminares, revelando a presença generalizada de alcaloides, juntamente com outras classes químicas. Todas as espécies estudadas são, portanto, potenciais candidatas para uso como herbicidas naturais.

Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan / Diversidade genética e caracterização molecular do Cucumber mosaic cucumovirus (CMV) subgrupo II infectando espinafre (Spinacia oleracea) e ervilha (Pisum sativum) na região de Pothwar, Paquistão

Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the [...].(AU)

Cucumber mosaic cucumovirus (CMV) é uma tremenda ameaça aos vegetais em todo o mundo, inclusive no Paquistão. O presente trabalho foi conduzido para investigar a variabilidade genética de isolados de CMV infectando vegetais de ervilha e espinafre na região de Pothwar, Paquistão. Pesquisas com base em sorologia durante 2016-2017 revelaram 31,70% da incidência geral da doença por CMV em safras de ervilha e espinafre. O ensaio de imunoabsorção enzimática em sanduíche de anticorpo triplo (TAS-ELISA) revelou que todos os isolados positivos pertencem ao subgrupo II do CMV. Dois cDNA selecionados de amostras positivas para ELISA representando cada safra de ervilha e espinafre foram amplificados por PCR (ca.1100 pb) e sequenciados correspondendo ao gene CMV CP que compartilhou 93,7% de identidade de nucleotídeo um com o outro. Ambas as sequências de isolados de ervilha CMV (AAHAP) e espinafre (AARS) do Paquistão foram submetidas ao GenBank como nos de acesso. MH119071 e MH119073, respectivamente. A análise BLAST revelou 93,4% de identidade de sequência do isolado AAHAP com SpK (KC763473) do Irã, enquanto o isolado AARS compartilhou a identidade máxima (94,5%) com a cepa 241 (AJ585519) da Austrália e agrupada com alguns isolados de referência do subgrupo II de CMV do Reino Unido (Z12818) e EUA (AF127976) em uma reconstrução filogenética vizinha. Um total de 59 sítios polimórficos (segregantes) (S) com diversidade de nucleotídeos (π) de 0,06218 foi evidente, enquanto nenhum evento INDEL foi observado em isolados do Paquistão. A distância evolutiva de isolados de CMV do Paquistão foi registrada como 0,0657 entre si e 0,0574-0,2964 com outros isolados de CMV relatados em outras partes do mundo. Um fluxo gênico frequente (Fst = 0,30478 < 0,33) foi observado entre os isolados de CMV do Paquistão e relatados anteriormente. Na análise de diferenciação genética, os valores de três testes estatísticos baseados em [...].(AU)

Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan / Diversidade genética e caracterização molecular do Cucumber mosaic cucumovirus (CMV) subgrupo II infectando espinafre (Spinacia oleracea) e ervilha (Pisum sativum) na região de Pothwar, Paquistão

Abstract Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour-joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the values 2.02535, 0.01468, and 0.71862 of Tajima's D, Fu, & Li's F* and D* respectively, demonstrating that the CMV population is under balancing selection.

Resumo Cucumber mosaic cucumovirus (CMV) é uma tremenda ameaça aos vegetais em todo o mundo, inclusive no Paquistão. O presente trabalho foi conduzido para investigar a variabilidade genética de isolados de CMV infectando vegetais de ervilha e espinafre na região de Pothwar, Paquistão. Pesquisas com base em sorologia durante 2016-2017 revelaram 31,70% da incidência geral da doença por CMV em safras de ervilha e espinafre. O ensaio de imunoabsorção enzimática em sanduíche de anticorpo triplo (TAS-ELISA) revelou que todos os isolados positivos pertencem ao subgrupo II do CMV. Dois cDNA selecionados de amostras positivas para ELISA representando cada safra de ervilha e espinafre foram amplificados por PCR (ca.1100 pb) e sequenciados correspondendo ao gene CMV CP que compartilhou 93,7% de identidade de nucleotídeo um com o outro. Ambas as sequências de isolados de ervilha CMV (AAHAP) e espinafre (AARS) do Paquistão foram submetidas ao GenBank como nos de acesso. MH119071 e MH119073, respectivamente. A análise BLAST revelou 93,4% de identidade de sequência do isolado AAHAP com SpK (KC763473) do Irã, enquanto o isolado AARS compartilhou a identidade máxima (94,5%) com a cepa 241 (AJ585519) da Austrália e agrupada com alguns isolados de referência do subgrupo II de CMV do Reino Unido (Z12818) e EUA (AF127976) em uma reconstrução filogenética vizinha. Um total de 59 sítios polimórficos (segregantes) (S) com diversidade de nucleotídeos (π) de 0,06218 foi evidente, enquanto nenhum evento INDEL foi observado em isolados do Paquistão. A distância evolutiva de isolados de CMV do Paquistão foi registrada como 0,0657 entre si e 0,0574-0,2964 com outros isolados de CMV relatados em outras partes do mundo. Um fluxo gênico frequente (Fst = 0,30478 < 0,33) foi observado entre os isolados de CMV do Paquistão e relatados anteriormente. Na análise de diferenciação genética, os valores de três testes estatísticos baseados em permutação viz, Z (84,3011), Snn (0,82456) e Ks * (4,04042) não foram significativos. A análise estatística revelou os valores 2,02535, 0,01468 e 0,71862 de Tajima's D, Fu, & Li's F * e D * respectivamente, demonstrando que a população de CMV está sob seleção de balanceamento.

Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan / Diversidade genética e caracterização molecular do Cucumber mosaic cucumovirus (CMV) subgrupo II infectando espinafre (Spinacia oleracea) e ervilha (Pisum sativum) na região de Pothwar, Paquistão

Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the [...].

Cucumber mosaic cucumovirus (CMV) é uma tremenda ameaça aos vegetais em todo o mundo, inclusive no Paquistão. O presente trabalho foi conduzido para investigar a variabilidade genética de isolados de CMV infectando vegetais de ervilha e espinafre na região de Pothwar, Paquistão. Pesquisas com base em sorologia durante 2016-2017 revelaram 31,70% da incidência geral da doença por CMV em safras de ervilha e espinafre. O ensaio de imunoabsorção enzimática em sanduíche de anticorpo triplo (TAS-ELISA) revelou que todos os isolados positivos pertencem ao subgrupo II do CMV. Dois cDNA selecionados de amostras positivas para ELISA representando cada safra de ervilha e espinafre foram amplificados por PCR (ca.1100 pb) e sequenciados correspondendo ao gene CMV CP que compartilhou 93,7% de identidade de nucleotídeo um com o outro. Ambas as sequências de isolados de ervilha CMV (AAHAP) e espinafre (AARS) do Paquistão foram submetidas ao GenBank como nos de acesso. MH119071 e MH119073, respectivamente. A análise BLAST revelou 93,4% de identidade de sequência do isolado AAHAP com SpK (KC763473) do Irã, enquanto o isolado AARS compartilhou a identidade máxima (94,5%) com a cepa 241 (AJ585519) da Austrália e agrupada com alguns isolados de referência do subgrupo II de CMV do Reino Unido (Z12818) e EUA (AF127976) em uma reconstrução filogenética vizinha. Um total de 59 sítios polimórficos (segregantes) (S) com diversidade de nucleotídeos (π) de 0,06218 foi evidente, enquanto nenhum evento INDEL foi observado em isolados do Paquistão. A distância evolutiva de isolados de CMV do Paquistão foi registrada como 0,0657 entre si e 0,0574-0,2964 com outros isolados de CMV relatados em outras partes do mundo. Um fluxo gênico frequente (Fst = 0,30478 < 0,33) foi observado entre os isolados de CMV do Paquistão e relatados anteriormente. Na análise de diferenciação genética, os valores de três testes estatísticos baseados em [...].

Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan

Abstract Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour-joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity () of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the values 2.02535, 0.01468, and 0.71862 of Tajima's D, Fu, & Lis F* and D* respectively, demonstrating that the CMV population is under balancing selection.

Resumo Cucumber mosaic cucumovirus (CMV) é uma tremenda ameaça aos vegetais em todo o mundo, inclusive no Paquistão. O presente trabalho foi conduzido para investigar a variabilidade genética de isolados de CMV infectando vegetais de ervilha e espinafre na região de Pothwar, Paquistão. Pesquisas com base em sorologia durante 2016-2017 revelaram 31,70% da incidência geral da doença por CMV em safras de ervilha e espinafre. O ensaio de imunoabsorção enzimática em sanduíche de anticorpo triplo (TAS-ELISA) revelou que todos os isolados positivos pertencem ao subgrupo II do CMV. Dois cDNA selecionados de amostras positivas para ELISA representando cada safra de ervilha e espinafre foram amplificados por PCR (ca.1100 pb) e sequenciados correspondendo ao gene CMV CP que compartilhou 93,7% de identidade de nucleotídeo um com o outro. Ambas as sequências de isolados de ervilha CMV (AAHAP) e espinafre (AARS) do Paquistão foram submetidas ao GenBank como nos de acesso. MH119071 e MH119073, respectivamente. A análise BLAST revelou 93,4% de identidade de sequência do isolado AAHAP com SpK (KC763473) do Irã, enquanto o isolado AARS compartilhou a identidade máxima (94,5%) com a cepa 241 (AJ585519) da Austrália e agrupada com alguns isolados de referência do subgrupo II de CMV do Reino Unido (Z12818) e EUA (AF127976) em uma reconstrução filogenética vizinha. Um total de 59 sítios polimórficos (segregantes) (S) com diversidade de nucleotídeos () de 0,06218 foi evidente, enquanto nenhum evento INDEL foi observado em isolados do Paquistão. A distância evolutiva de isolados de CMV do Paquistão foi registrada como 0,0657 entre si e 0,0574-0,2964 com outros isolados de CMV relatados em outras partes do mundo. Um fluxo gênico frequente (Fst = 0,30478 0,33) foi observado entre os isolados de CMV do Paquistão e relatados anteriormente. Na análise de diferenciação genética, os valores de três testes estatísticos baseados em permutação viz, Z (84,3011), Snn (0,82456) e Ks * (4,04042) não foram significativos. A análise estatística revelou os valores 2,02535, 0,01468 e 0,71862 de Tajimas D, Fu, & Lis F * e D * respectivamente, demonstrando que a população de CMV está sob seleção de balanceamento.

The Isolation, Structure Elucidation and Bioactivity Study of Chilensosides A, A1, B, C, and D, Holostane Triterpene Di-, Tri- and Tetrasulfated Pentaosides from the Sea Cucumber Paracaudina chilensis (Caudinidae, Molpadida).

Five new triterpene (4,4,14-trimethylsterol) di-, tri- and tetrasulfated pentaosides, chilensosides A (1), A1 (2), B (3), C (4), and D (5) were isolated from the Far-Eastern sea cucumber Paracaudina chilensis. The structures were established on the basis of extensive analysis of 1D and 2D NMR spectra and confirmed by HR-ESI-MS data. The structural variability of the glycosides concerned the pentasaccharide chains. Their architecture was characterized by the upper semi-chain consisting of three sugar units and the bottom semi-chain of two sugars. Carbohydrate chains of compounds 2-5 differed in the quantity and positions of sulfate groups. The interesting structural features of the glycosides were: the presence of two sulfate groups at C-4 and C-6 of the same glucose residue in the upper semi-chain of 1, 2, 4, and 5 and the sulfation at C-3 of terminal glucose residue in the bottom semi-chain of 4 that makes its further elongation impossible. Chilensoside D (5) was the sixth tetrasulfated glycoside found in sea cucumbers. The architecture of the sugar chains of chilensosides A-D (1-5), the positions of sulfation, the quantity of sulfate groups, as well as the aglycone structures, demonstrate their similarity to the glycosides of the representatives of the order Dendrochirotida, confirming the phylogenetic closeness of the orders Molpadida and Dendrochirotida. The cytotoxic activities of the compounds 1-5 against human erythrocytes and some cancer cell lines are presented. Disulfated chilensosides A1 (2) and B (3) and trisulfated chilensoside C (4) showed significant cytotoxic activity against human cancer cells.

First Report of Fusarium verticillioides Causing Cucumber Fruit Rot in Sinaloa, Mexico.

Cucumber (Cucumis sativus L.) is a fruit crop with high consumption worldwide. Mexico had a cucumber production of 826,485 tonnes in 2019. In December 2020, in a greenhouse in Sinaloa State, 18% of persian cucumber fruits with rot symptoms and the development of cottony white mycelia at both ends were observed similar to those described for Fusarium incarnatum (Garcia-Estrada et al., 2021). Isolation of the causal agent was carried out on PDA medium at 27°C for seven days from disinfested sections of cucumber tissues in NaOCl at 1% for one minute and then rinsed in distilled water. Morphological characterization was carried out on SNA medium, in which cultures was colorless and showed scarcely mycelia growth; however, microconidia were abundant and mainly showed clavate shaped measuring 16.6±2.2 x 5.32±1.0 µm (n=100). The morphological characteristics were similar to those described for Fusarium verticillioides (Nirenberhg, 1981). To confirm the species identity, the internal transcribed spacer (ITS) region and the actin (ACT), ß-tubulin (B-tub), calmodulin (CAL), and translation elongation factor 1-α (TEF1-α) genes were amplified and sequenced from one representative isolate: FPM03. These sequences were submitted to GenBank with the accession number MZ868200 for the ITS region and MZ955274 to MZ955277 for the ACT, B-tub, CAL, and TEF1-α regions. BLASTn analysis of the sequences showed 99 to 100% identity with several F. verticillioides sequence accession numbers MG515226, KU603765, MW402311, MW402449, and MW402113, which corresponded to strains CM1, CBS 576.78, and CBS 218.76. To evaluate Koch's postulates, ten healthy cucumber fruits were disinfected with 1% NaOCl for one min and then washed with distilled water. The fruits were inoculated with a single-spore suspension (3 × 104 conidia/mL) by spraying, as well as, five two-month-old cucumber plants. For controls, ten cucumber fruits and five plants were sprayed with sterile distilled water. All fruits were incubated in plastic bags at 25°C for four days and plants were placed under greenhouses conditions for a week. At 30 h after inoculation, all inoculated fruits showed soft rot symptoms at the fruit poles, and the development of white and cottony mycelia was observed at 48 h. Inoculated plants showed the symptoms mainly in the flower end of the fruits after three days. The symptoms observed under laboratory conditions were similar to those registered initially in the field. Samples of rotted tissues (fruit ends and flowers) from inoculated fruits were cultured on PDA medium; the resultant colonies showed similar characteristics to those obtained initially and the same pathogen was recovered. All control fruits and plants remained healthy, confirming pathogenicity. Fusarium verticillioides is primarily a maize pathogen causing stalk and ear rots globally, resulting in significant yield losses and reductions in grain quality; besides, this species produces large amounts of fumonisin B1 with high toxigenicity and is frequently found as food contaminant (Leslie and Sumerell, 2006). In addition, this pathogen was reported to affect sweet sorghum in Spain and banana in Jordan (Palmero et al., 2012; Salem et al., 2020). Recently, in Mexico, F. incarnatum was reported to cause soft rot in cucumber fruits (Garcia-Estrada et al., 2021); however, this is the first report of F. verticillioides affecting Mexican cucumber production. This information will be relevant for disease prevention and control.

Selection and evaluation of suitable reference genes for quantitative gene expression analysis during infection of Cucumis sativus with Pectobacterium brasiliense.

AIMS: Bacterial soft rot caused by Pectobacterium brasiliense (Pbr) has resulted in severe economic losses of cucumber production in northern China. Quantitative reverse transcription PCR (RT-qPCR) is widely used to determine the fold change in the expression of genes of interest, and an appropriate reference gene played a critical role in the evaluation of genes expression. However, the suitable reference genes for transcript normalization during the interaction between cucumber and Pbr have not yet been systematically validated. In this study, we aimed to identify the suitable reference genes for accurate and reliable normalization of cucumber and Pbr RT-qPCR data. METHODS AND RESULTS: We selected 14 candidate reference genes for cucumber and 10 candidate reference genes for Pbr were analysed by using four algorithms (the deltaCt method, BestKeeper, NormFinder and geNorm). Furthermore, five genes in cucumber involved in plant resistance and five genes in Pbr related to the virulence were selected to confirm the reliability of the reference genes by RT-qPCR. CsARF (ADP-ribosylation factor 1) and pgi (glucose-6-phosphate isomerase) were suggested as the most suitable reference genes for cucumber and Pbr respectively. CONCLUSION: Our results suggested that CsARF (ADP-ribosylation factor 1) and pgi (glucose-6-phosphate isomerase) could be as the reference genes to normalize expression data for cucumber and Pbr during the process of pathogen-host interaction respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: To our knowledge, this is the first systematic study of the optimal reference genes specific to cucumber and Pbr, which could help advance the molecular interactions research in Cucurbitaceae vegetables and Pectobacterium species pathosystems.

Importance of deepening integration of crime and conservation sciences.

Conservation crime is a globally distributed societal problem. Conservation crime science, an emerging interdisciplinary field, has the potential to help address this problem. However, its utility depends on serious reflection on the transposition of crime science approaches to conservation contexts, which may differ in meaningful ways from traditional crime contexts. We considered the breadth of crime science approaches being used in conservation as well as the depth of crime science integration in conservation. We used the case of sea cucumber (Holothuria floridana, Isostichopus badionotus) trafficking in Mexico as an example of why the interdisciplinarity of crime and conservation sciences should be deepened and how integration can help ideate new solutions. We first conducted a review of literature to capture the range of interdisciplinarity applications. We identified 6 crime science approaches being applied to the conservation contexts of illegal, unreported, and unregulated fishing; wildlife and plant crime; and illegal logging. We then compared this knowledge base to the case of illegal sea cucumber fishing in Mexico. We identified 5 challenges in the application of these approaches to conservation contexts: the relative diffusion of harms and victims in conservation crimes; scalar mismatches in crime, authority, and the conservation issue itself; interactions between legal and illegal networks; communities and their authority to define and control crime; and the role of natural science in the rule of law. Considering these 5 factors may enhance the depth of interdisciplinarity between crime and conservation sciences. Nurturing interdisciplinary crime and conservation science will expand innovation and help accelerate successful risk management programs and other policy agendas.

La Importancia de Profundizar la Integración de las Ciencias Criminológicas y de la Conservación Gore & Bennett Resumen El crimen en conservación es un problema social distribuido globalmente. La ciencia criminológica de la conservación, un campo interdisciplinario emergente, tiene el potencial para contribuir a atender este problema. Sin embargo, su utilidad depende de la reflexión seria sobre la transposición de los métodos de la ciencia criminológica en el contexto de la conservación, que puede diferir de forma significativa de los de contextos tradicionales del crimen. Consideramos la gama de métodos de las ciencias criminológicas que están siendo utilizadas en conservación, así como la profundidad de la integración de la ciencia criminológica en la conservación. Utilizamos el caso del tráfico de pepino de mar (Holothuria floridana, Isostichopus badionotus) en México como un ejemplo de porqué la interdisciplinaridad de las ciencias criminológicas y de conservación debería profundizarse y de cómo puede la integración ayudar a idear nuevas soluciones. Primero hicimos una revisión de literatura para capturar el rango de aplicaciones interdisciplinarias. Identificamos que 6 métodos de ciencia criminológica fueron aplicados en contextos de conservación de pesca ilegal, no registrada y no regulada, crimen con fauna y plantas silvestres y tala ilegal. Posteriormente comparamos esta base de conocimiento al caso de la pesca ilegal de pepino de mar en México. Identificamos 5 retos en la aplicación de estos métodos en contextos de conservación: la difusión relativa de daños y víctimas en crímenes de conservación; desajustes escalares en el crimen, la autoridad y el tema de la conservación misma; interacciones entre redes legales e ilegales; comunidades y su autoridad para definir y controlar el crimen; y el papel de las ciencias naturales en el estado de derecho. Considerar estos 5 factores puede aumentar la profundidad de la interdisciplinaridad entre las ciencias criminológicas y de la conservación. Fomentar la ciencia criminológica y de conservación interdisciplinaria ampliará la innovación y ayudará a acelerar los programas exitosos de gestión de riesgos y otras agendas políticas.

On the effects of temperature and pH on tropical and temperate holothurians.

Ocean acidification and increased ocean heat content has direct and indirect effects on marine organisms such as holothurians (sea cucumbers) that are vulnerable to changes in pH and temperature. These environmental factors have the potential to influence organismal performance and fitness at different life stages. Tropical and temperate holothurians are more vulnerable to temperature and pH than those from colder water environments. The high level of environmental variation observed in the oceans could influence organismal responses and even produce a wide spectrum of compensatory physiological mechanisms. It is possible that in these areas, larval survival will decline by up to 50% in response to a reduction of 0.5 pH units. Such reduction in pH may trigger low intrinsic growth rates and affect the sustainability of the resource. Here we describe the individual and combined effects that temperature and pH could produce in these organisms. We also describe how these effects can scale from individuals to the population level by using age-structured spatial models in which depensation can be integrated. The approach shows how physiology can improve the conservation of the resource based on the restriction of growth model parameters and by including a density threshold, below which the fitness of the population, specifically intrinsic growth rate, decreases.

Feeding habits of Holothuria (Stauropora) fuscocinerea (Echinodermata: Holothuroidea) in a Mexican Pacific reef / Hábitos alimenticios de Holothuria (Stauropora) fuscocinerea (Echinodermata: Holothuroidea) en un arrecife del Pacífico Mexicano

Introduction: The importance of holothuroids in marine ecosystems is related to their feeding activities, which have been little studied in the eastern Pacific. Objective: To describe the feeding habits of the sea cucumber Holothuria (Stauropora) fuscocinerea and their bioturbation potential in La Entrega reef, México. Methods: The population size of H. (Stauropora) fuscocinerea was determined by means of four 20 x 4 m (320 m2) band transects, while the available sediment for the sea cucumbers and their feces were characterized in three stations (A-C) via granulometry and quantification of organic carbon and organic matter. Excretion rate was determined every 4 hr over a 24 hr period and the relationship between sea cucumber length and biomass and the excretion rate evaluated. Results: According to non-parametric permutation, ordination and percentage similarity analyses, sea cucumber feces mostly comprised a large proportion of small grains compared to the available sediment, indicating that H. (Stauropora) fuscocinerea is selective on grain size. Preliminary bioturbation potential of the species may reach up to 8.71 ± 0.17 kg day of sediment in the study area. Conclusion: The spatial distribution of H. (Stauropora) fuscocinerea in the study area is a product of its selective feeding activity, evidencing the preliminary importance of the species in the trophic dynamics of La Entrega reef.

Introducción: La relevancia de los holoturoideos en los ecosistemas marinos está relacionada con sus actividades alimenticias, las cuales han sido escasamente estudiadas en el Pacífico oriental. Objetivo: Describir los hábitos alimenticios del pepino de mar Holothuria (Stauropora) fuscocinerea y su potencial de bioturbación en el arrecife La Entrega, México. Métodos: Se determinó el tamaño poblacional de H. (Stauropora) fuscocinerea mediante cuatro transectos de banda de 20 x 4 m (320 m2), mientras que la caracterización de los sedimentos disponibles y las heces de los pepinos se realizó en tres estaciones (A-C) mediante granulometría y cuantificación de carbono orgánico y materia orgánica. Se determinó la tasa de excreción cada 4 hr durante un periodo de 24 hr y se evaluó la relación entre la talla y la biomasa con la tasa de excreción. Resultados: De acuerdo con un análisis no paramétrico mediante permutaciones, ordenación y similitud, las heces de los pepinos estuvieron compuestas en su mayoría por una gran cantidad de granos pequeños en comparación con el sedimento disponible, lo que sugiere que H. (Stauropora) fuscocinerea es una especie selectiva respecto al tamaño de grano. El potencial de bioturbación preliminar de la especie puede alcanzar 8.71 ± 0.17 kg día en el área de estudio. Conclusiones: La distribución espacial de H. (Stauropora) fuscocinerea en el área de estudio es producto de su selectividad alimenticia, evidenciando la importancia de la especie en la dinámica trófica del arrecife La Entrega.

Primer registro del género Leptopentacta (Cucumariidae: Colochirinae) en el Caribe nicaragüense / First record of the genus Leptopentacta (Cucumariidae: Colochirinae) for the Nicaraguan Caribbean

Introducción: El género Leptopentacta solo ha sido reportado previamente en Florida, Cuba, Colombia, Costa Rica y Surinam. Objetivo: Presentar el primer registro del género para Nicaragua. Métodos: Los caracteres morfológicos del material nicaragüense del Smithsonian Institution (USNM 1014529), fueron corroborados con la descripción original. Resultados: Los cinco especímenes recolectados en el Caribe nicaragüense coinciden con el género. Conclusiones: Leptopentacta se reporta por primera vez en el Mar Caribe de Nicaragua. Esto aumenta el número de equinodermos nicaragüenses a 194 especies.

Introduction: The genus Leptopentacta has only been previously reported from Florida, Cuba, Colombia, Costa Rica, and Suriname. Objective: To present the first record of the genus for Nicaragua. Methods: The morphological characters of Nicaraguan material at the Smithsonian Institution (USNM 1014529), were corroborated with the original description. Results: The five specimens collected in the Nicaraguan Caribbean match the genus. Conclusions: Leptopentacta is reported for the first time from the Nicaraguan Caribbean Sea. This increases the number of Nicaraguan echinoderms to 194 species.

The Role of the Microbiota in Regeneration-Associated Processes.

The microbiota, the set of microorganisms associated with a particular environment or host, has acquired a prominent role in the study of many physiological and developmental processes. Among these, is the relationship between the microbiota and regenerative processes in various organisms. Here we introduce the concept of the microbiota and its involvement in regeneration-related cellular events. We then review the role of the microbiota in regenerative models that extend from the repair of tissue layers to the regeneration of complete organs or animals. We highlight the role of the microbiota in the digestive tract, since it accounts for a significant percentage of an animal microbiota, and at the same time provides an outstanding system to study microbiota effects on regeneration. Lastly, while this review serves to highlight echinoderms, primarily holothuroids, as models for regeneration studies, it also provides multiple examples of microbiota-related interactions in other processes in different organisms.

RNA Interference on Regenerating Holothurian Gut Tissues.

Functional studies on echinoderms have been reduced to the use of pharmacological treatments. The ability to modulate the genetic expression of regenerating tissues can elucidate potential effectors during this process. Here we describe an effective transfection protocol that allows the introduction of Dicer-substrate interference RNAs (DsiRNAs) for the modulation of gene expression and its characterization during regeneration.

Illegal fisheries, environmental crime, and the conservation of marine resources.

The illegal harvest of marine species within exclusive economic zones can have a strong impact on the function of local ecosystems and livelihoods of coastal communities. The complexity of these problems is often overlooked in the development of solutions, leading to ineffective and sometimes harmful social and environmental outcomes. One-dimensional, oversimplified perspectives can lead to conservation prescriptions that exacerbate social stressors. This is particularly critical in the case of international illegal trade of endangered, high-value species, which generate a value chain in which artisanal fishers are the first operational and often the weakest link of an intricate web. We examined 2 illegal fisheries, totoaba (Totoaba macdonaldi) and sea cucumber (Isostichopus badionotus and Holothuria floridana), in Mexico. Although these are 2 separate and independent fisheries, important ecological (resource condition, fishery impacts at the ecosystem level) and social (governance, markets) similarities improve understanding of their complexity. Our findings are relevant globally and show the need for interdisciplinary decision-making groups, community engagement, and the development of demand reduction measures.

Pesquerías Ilegales, Crímenes Ambientales y la Conservación de los Recursos Marinos Resumen La cosecha ilegal de especies marinas dentro de las zonas económicas exclusivas puede tener un impacto serio sobre la función de los ecosistemas locales y el economia de las comunidades costeras. La complejidad de estos problemas generalmente se ignora durante el desarrollo de soluciones, lo que conlleva a resultados ambientales y sociales poco efectivos y algunas veces dañinos. Las perspectivas unidimensionales y sobresimplificadas pueden derivar en prescripciones de conservación que empeoran las condiciones sociales sociales. Lo anterior es particularmente crítico para el caso del mercado ilegal de especies en peligro y de alto valor, lo que genera una cadena de valores en la que los pescadores tradicionales son el primer eslabón operativo y con frecuencia el más débil de una red intrincada. Examinamos dos pesquerías ilegales, la de la totoaba (Totoaba macdonaldi) y la del pepino de mar (Isostichopus badionotus y Holothuria floridana), en México. Aunque estas dos pesquerías son diferentes e independientes, las importantes similitudes ecológicas (estado del recurso, impactos de la pesquería a nivel de ecosistema) y sociales (governancia, mercados) mejoran el conocimiento de su complejidad. Nuestros hallazgos son relevantes a escala global y muestran la necesidad de tener grupos interdisciplinarios para tomar decisiones, la participación de la comunidad y el desarrollo de medidas para reducir la demanda por el producto pesquero.