Transcriptome analysis of the spider Phonotimpus pennimani reveals novel toxin transcripts.

Background: Phonotimpus pennimani (Araneae, Phrurolithidae) is a small-sized (3-5 mm) spider endemic to the Tacaná volcano in Chiapas, Mexico, where it is found in soil litter of cloud forests and coffee plantations. Its venom composition has so far not been investigated, partly because it is not a species of medical significance. However, it does have an important impact on the arthropod populations of its natural habitat. Methods: Specimens were collected in Southeastern Mexico (Chiapas) and identified taxonomically by morphological characteristics. A partial sequence from the mitochondrial gene coxI was amplified. Sequencing on the Illumina platform of a transcriptome library constructed from 12 adult specimens revealed 25 toxin or toxin-like genes. Transcripts were validated (RT-qPCR) by assessing the differential expression of the toxin-like PpenTox1 transcript and normalising with housekeeping genes. Results: Analysis of the coxI-gene revealed a similarity to other species of the family Phrurolithidae. Transcriptome analysis also revealed similarity with venom components of species from the families Ctenidae, Lycosidae, and Sicariidae. Expression of the toxin-like PpenTox1 gene was different for each developmental stage (juvenile or adult) and also for both sexes (female or male). Additionally, a partial sequence was obtained for the toxin-like PpenTox1 from DNA. Conclusion: Data from the amplification of the mitochondrial coxI gene confirmed that P. pennimani belongs to the family Phrurolithidae. New genes and transcripts coding for venom components were identified.

Scheduling mobile dental clinics: A heuristic approach considering fairness among school districts.

Mobile dental clinics (MDCs) are suitable solutions for servicing people living in rural and urban areas that require dental healthcare. MDCs can provide dental care to the most vulnerable high-school students. However, scheduling MDCs to visit patients is critical to developing efficient dental programs. Here, we study a mobile dental clinic scheduling problem that arises from the real-life logistics management challenge faced by a school-based mobile dental care program in Southern Chile. This problem involves scheduling MDCs to treat high-school students at public schools while considering a fairness constraint among districts. Schools are circumscribed into districts, and by program regulations, at least 50% of the students in each district must receive dental care during the first semester. Fairness prevents some districts from waiting more time to receive dental care than others. We model the problem as a parallel machine scheduling problem with sequence-dependent setup costs and batch due dates and propose a mathematical model and a genetic algorithm-based solution to solve the problem. Our computational results demonstrate the effectiveness of our approaches in obtaining near-optimal solutions. Finally, dental program managers can use the methodologies presented in this work to schedule mobile dental clinics and improve their operations.

The guardstone spiders of the genus Phonotimpus Gertsch & Davis (Araneae: Phrurolithidae) from northeastern Mexico.

The American genus Phonotimpus Gertsch & Davis, 1940 (Araneae, Phrurolithidae) was described on the basis of two species from northern Mexico. Recently, four species were described from Central and South Mexico and one species was transferred to this genus. Here we describe the males of Phonotimpus separatus Gertsch & Davis (the type species) and P. eutypus Gertsch & Davis, both previously known only from female specimens. Moreover, we describe 25 new species from Northeast Mexico (Nuevo León, Tamaulipas, and San Luis Potosí): P. ahuacatlan sp. nov., P. arcitos sp. nov., P. boneti sp. nov., P. calenturas sp. nov., P. chipinque sp. nov., P. cielo sp. nov., P. cima sp. nov., P. cuauhtemoc sp. nov., P. cumbres sp. nov., P. elviejo sp. nov., P. escondida sp. nov., P. farias sp. nov., P. frio sp. nov., P. gertschi sp. nov., P. llera sp. nov., P. perra sp. nov., P. pozas sp. nov., P. puente sp. nov., P. revilla sp. nov., P. sanpedro sp. nov., P. vacas sp. nov., P. valles sp. nov., P. taman sp. nov., P. tetrico sp. nov. and P. xilitla sp. nov. Furthermore, we propose five species groups that include almost all of the new species and all the species described to date.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.).

BACKGROUND: Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. RESULTS: Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. CONCLUSIONS: Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

A new species of the genus Phonotimpus Gertsch amp; Davis (Araneae: Phrurolithidae) from Mexico and the transfer of Gosiphrurus schulzefenai Chamberlin amp; Ivie to Phonotimpus.

Phonotimpus padillai sp. nov. is described on the basis of morphological characteristics of both sexes: males are easily distinguished by the shape of the embolus and females by the shape of the copulatory openings. Additionally, Gosiphrurus schulzefenai Chamberlin Ivie, 1936 is transferred to the genus Phonotimpus Gertsch Davis, 1940, based on the redescription of the female and first description of the male, with an update of the diagnosis of this species.

Co-occurrence of cohesin complex and Ras signaling mutations during progression from myelodysplastic syndromes to secondary acute myeloid leukemia.

Myelodysplastic syndromes (MDS) are hematological disorders at high risk of progression to secondary acute myeloid leukemia (sAML). However, the mutational dynamics and clonal evolution underlying disease progression are poorly understood at present. To elucidate the mutational dynamics of pathways and genes occurring during the evolution to sAML, next generation sequencing was performed on 84 serially paired samples of MDS patients who developed sAML (discovery cohort) and 14 paired samples from MDS patients who did not progress to sAML during follow-up (control cohort). Results were validated in an independent series of 388 MDS patients (validation cohort). We used an integrative analysis to identify how mutations, alone or in combination, contribute to leukemic transformation. The study showed that MDS progression to sAML is characterized by greater genomic instability and the presence of several types of mutational dynamics, highlighting increasing (STAG2) and newly-acquired (NRAS and FLT3) mutations. Moreover, we observed cooperation between genes involved in the cohesin and Ras pathways in 15-20% of MDS patients who evolved to sAML, as well as a high proportion of newly acquired or increasing mutations in the chromatin-modifier genes in MDS patients receiving a disease-modifying therapy before their progression to sAML.

Four new species of the genus Novalena Chamberlin amp; Ivie, 1942 (Araneae: Agelenidae) from southeastern Mexican montane forests and first record of ocular anomaly in the genus.

Four new species of the spider genus Novalena Chamberlin Ivie, 1942 are described: N. bola sp. nov., N. mayae sp. nov., N. padillai sp. nov., and N. zootaxa sp. nov. All species were collected in montane forests in Chiapas, Mexico, and three of them occur in sympatry across their distribution range.

Alternative management for gynecological cancer care during the COVID-2019 pandemic: A Latin American survey.

OBJECTIVE: To determine the acceptance rate of treatment alternatives for women with either preinvasive conditions or gynecologic cancers during the COVID-19 pandemic among Latin American gynecological cancer specialists. METHODS: Twelve experts in gynecological cancer designed an electronic survey, according to recommendations from international societies, using an online platform. The survey included 22 questions on five topics: consultation care, preinvasive cervical pathology, and cervical, ovarian, and endometrial cancer. The questionnaire was distributed to 1052 specialists in 14 Latin American countries. A descriptive analysis was carried out using statistical software. RESULTS: A total of 610 responses were received, for an overall response rate of 58.0%. Respondents favored offering teleconsultation as triage for post-cancer treatment follow-up (94.6%), neoadjuvant chemotherapy in advanced stage epithelial ovarian cancer (95.6%), and total hysterectomy with bilateral salpingo-oophorectomy and defining adjuvant treatment with histopathological features in early stage endometrial cancer (85.4%). Other questions showed agreement rates of over 64%, except for review of pathology results in person and use of upfront concurrent chemoradiation for early stage cervical cancer (disagreement 56.4% and 58.9%, respectively). CONCLUSION: Latin American specialists accepted some alternative management strategies for gynecological cancer care during the COVID-19 pandemic, which may reflect the region's particularities. The COVID-19 pandemic led Latin American specialists to accept alternative management strategies for gynecological cancer care, especially regarding surgical decisions.

Diversity and seasonal variation of ground and understory spiders from a tropical mountain cloud forest.

We made intensive samplings to study the seasonal response of spiders across different forest strata (ground and understory) in a tropical mountain cloud forest from Mexico. We sampled spiders from ten plots in six sampling events during the dry and rainy season, to analyze their abundance, structure (distribution of abundance among species), diversity and the response of the five dominant species at each stratum. Results demonstrated that seasonal patterns of spider communities differed among strata, revealing a complex spatiotemporal dynamic. Abundance, structure, diversity of ground spiders, as well as the responses of four dominant species at this stratum, showed low seasonal variations. In contrast, a strong seasonal variation was observed for the understory assemblage, with lowest abundance and highest diversity in the rainy season, and different assemblage structures for each season. Seasonal patterns of each assemblage seem linked to the responses of their dominant species. We found high co-occurrence among most of the ground dominant species with similar habitat use and with multivoltine patterns, contrasting with low co-occurrence among most of the understory dominant species with similar habitat use and univoltine patterns. Our results showed that the spiders' assemblages of tropical mountain cloud forest (opposed to what is found in temperate and boreal forests) increase their species richness with the height, and that their responses to seasonal change differ between strata. Management programs of these habitats should consider the spatial and temporal variations found here, as a better understanding of their ecological dynamics is required to support their sustainable management.

Plant Microbial Fuel Cells⁻Based Energy Harvester System for Self-powered IoT Applications.

The emergence of modern technologies, such as Wireless Sensor Networks (WSNs), the Internet-of-Things (IoT), and Machine-to-Machine (M2M) communications, involves the use of batteries, which pose a serious environmental risk, with billions of batteries disposed of every year. However, the combination of sensors and wireless communication devices is extremely power-hungry. Energy Harvesting (EH) is fundamental in enabling the use of low-power electronic devices that derive their energy from external sources, such as Microbial Fuel Cells (MFC), solar power, thermal and kinetic energy, among others. Plant Microbial Fuel Cell (PMFC) is a prominent clean energy source and a step towards the development of self-powered systems in indoor and outdoor environments. One of the main challenges with PMFCs is the dynamic power supply, dynamic charging rates and low-energy supply. In this paper, a PMFC-based energy harvester system is proposed for the implementation of autonomous self-powered sensor nodes with IoT and cloud-based service communication protocols. The PMFC design is specifically adapted with the proposed EH circuit for the implementation of IoT-WSN based applications. The PMFC-EH system has a maximum power point at 0.71 V, a current density of 5 mA cm - 2 , and a power density of 3.5 mW cm - 2 with a single plant. Considering a sensor node with a current consumption of 0.35 mA, the PMFC-EH green energy system allows a power autonomy for real-time data processing of IoT-based low-power WSN systems.

A new species of Phonotimpus Gertsch Davis, 1940 (Araneae: Phrurolithidae) from Mexico.

The genus Phonotimpus Gertsch Davis, 1940 includes four species all known only from Mexico (World Spider Catalog 2018). P. separatus and P. eutypus were described by Gertsch Davis (1940) from San Luis Potosí and from Nuevo León, respectively. Phonotimpus pennimani and P. talquian, described by Chamé-Vázquez, Ibarra-Núñez Jiménez (2018), are the southernmost species in this genus (Chamé-Vázquez et al. 2018), and have restricted allopatric geographic distributions in Chiapas. This genus differs from other American phrurolithid genera by the following combination of characters: posterior eye row recurved, posterior median eyes closer to posterior lateral eyes than to each other, posterior median eyes smaller than posterior lateral eyes, females with dorsal scutum on the opisthosoma; palpi of males with retrolateral and dorsal tibial apophyses not joined at the base, and copulatory bulb with a conductor, embolus and embolar basal process (Gertsch Davis 1940; Penniman 1985; Chamé-Vázquez et al. 2018). In this paper, a new species of Phonotimpus is described and illustrated, based on specimens collected in soil of a pine-oak forest in the state of Mexico.

A new species of the spider genus Wirada (Araneae, Theridiidae) from Mexico, with taxonomic notes on the genus and a key to the species.

Wirada Keyserling, 1886 is one of the smallest genera of Theridiidae with only five South American species (World Spider Catalog 2018). Keyserling (1886) described first Wirada punctata (male) from Peru. Simon (1895) described W. rugithorax and W. tovarensis (males) from Venezuela, but Levi (1963) synonymized W. rugithorax with W. punctata. Later, Levi (1967) described W. tijuca (male) from southeastern Brazil, and lately Lise et al. (2009) described W. sigillata Lise, Silva Bertocello, 2009 and W. araucaria Lise, Silva Bertocello, 2009 (males and females) from southern Brazil. Simon (1894) placed Wirada in its group Histogonieae, and stated it is close to Pholcommateae. Until now, none species of Wirada has been included in any phylogenetic study of Theridiidae, only Agnarsson (2004) when commented the Pholcommatinae said "Based on the synapomorphies of the group it is likely that ... Wirada belong to this subfamily." Recently, this genus was reported (as Wirada sp1) from two localities in Mexico (Ibarra et al. 2011; Álvarez-Padilla 2015; Rivera-Quiroz et al. 2016) and subsequent samplings on three other sites from Chiapas (Campuzano et al. 2016) exposed more specimens. After examining these specimens, we found they do not match any of the known species and therefore we propose a new species. We also include taxonomic and biological notes about the genus and a key to the species.

Redescription of Phonotimpus separatus Gertsch Davis, 1940 (Araneae: Phrurolithidae) and description of two new species of Phonotimpus from Mexico.

The female of Phonotimpus separatus Gertsch Davis (the type species of the genus) is redescribed from a specimen collected at the type locality, and two new species of Phonotimpus from Mexico are described: P. pennimani sp. nov. and P. talquian sp. nov. A more detailed description of P. separatus is provided to better distinguish them from related taxa. The two new species are closely related; males and females of both species share several somatic and genitalic characters not found in P. separatus. The resemblance of both new species to P. separatus is discussed.

Peliosis hepatis associated with follicular lymphoma with a rise in vascular endothelial growth factor and anaemia of inflammation.

Follicular lymphoma does not usually present with associated paraneoplastic syndromes. We describe the case of a patient diagnosed with follicular lymphoma when investigating anaemia of chronic disease/inflammation and who, during her clinical course, developed peliosis hepatis. We have been able to confirm the similarity between the symptoms, the tumour's biology, the anaemia and peliosis, with the behaviour of endothelial growth factor, interleukins and iron metabolism disorders, which were normalised with treatment. To date, we have found no cases where peliosis has been described in this type of lymphoma.

Next-generation sequencing and FISH studies reveal the appearance of gene mutations and chromosomal abnormalities in hematopoietic progenitors in chronic lymphocytic leukemia.

BACKGROUND: Chronic lymphocytic leukemia (CLL) is a highly genetically heterogeneous disease. Although CLL has been traditionally considered as a mature B cell leukemia, few independent studies have shown that the genetic alterations may appear in CD34+ hematopoietic progenitors. However, the presence of both chromosomal aberrations and gene mutations in CD34+ cells from the same patients has not been explored. METHODS: Amplicon-based deep next-generation sequencing (NGS) studies were carried out in magnetically activated-cell-sorting separated CD19+ mature B lymphocytes and CD34+ hematopoietic progenitors (n = 56) to study the mutational status of TP53, NOTCH1, SF3B1, FBXW7, MYD88, and XPO1 genes. In addition, ultra-deep NGS was performed in a subset of seven patients to determine the presence of mutations in flow-sorted CD34+CD19- early hematopoietic progenitors. Fluorescence in situ hybridization (FISH) studies were performed in the CD34+ cells from nine patients of the cohort to examine the presence of cytogenetic abnormalities. RESULTS: NGS studies revealed a total of 28 mutations in 24 CLL patients. Interestingly, 15 of them also showed the same mutations in their corresponding whole population of CD34+ progenitors. The majority of NOTCH1 (7/9) and XPO1 (4/4) mutations presented a similar mutational burden in both cell fractions; by contrast, mutations of TP53 (2/2), FBXW7 (2/2), and SF3B1 (3/4) showed lower mutational allele frequencies, or even none, in the CD34+ cells compared with the CD19+ population. Ultra-deep NGS confirmed the presence of FBXW7, MYD88, NOTCH1, and XPO1 mutations in the subpopulation of CD34+CD19- early hematopoietic progenitors (6/7). Furthermore, FISH studies showed the presence of 11q and 13q deletions (2/2 and 3/5, respectively) in CD34+ progenitors but the absence of IGH cytogenetic alterations (0/2) in the CD34+ cells. Combining all the results from NGS and FISH, a model of the appearance and expansion of genetic alterations in CLL was derived, suggesting that most of the genetic events appear on the hematopoietic progenitors, although these mutations could induce the beginning of tumoral cell expansion at different stage of B cell differentiation. CONCLUSIONS: Our study showed the presence of both gene mutations and chromosomal abnormalities in early hematopoietic progenitor cells from CLL patients.

Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes.

To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.

Genetic variability and phylogeny analysis of partial L1 gene of human papillomavirus variants in Buenos Aires, Argentina.

In the present study, the molecular characterization of HPV variants 16, 18, 31, 58, 6 and 11 within the MY06/MY11 L1 genomic region was performed in 128 sequences. For HPV 16, all of the sequences analyzed had a 3 nucleotide insertion resulting in the insertion of serine in the L1 protein sequence; and 4 sequences had at least one single nucleotide polymorphism (SNP). Twelve base substitutions were detected in HPV 58, 6 SNPs produced amino acid changes, and the other SNPs detected were found to be silent mutations. For HPV 31, 25 SNPs were detected as silent mutations. Of the 8 SNPs detected on HPV 18, three produced amino acid changes, the remaining SNPs detected were silent mutations. For HPV 6, 10 SNPs were detected and none of them produced amino acid changes. From the 16 sequences analyzed for HPV 11, two SNPs were detected and neither of them produced amino acid substitutions. Phylogenetic trees were constructed for HPV 16, HPV 18, HPV 31, HPV 58, HPV 6 and HPV 11. In the current study 8 new variants were identified based on sequencing of the L1 region. Changes in the L1 region of the HPV genome may be important for discriminating the infectious potential of different variants, as well as in defining epitopes relevant to vaccine design. The findings of this study indicate that there are new variants of HPV circulating in Argentina, which need to be confirmed by further analyses of the complete HPV genome.

A Low Frequency of Losses in 11q Chromosome Is Associated with Better Outcome and Lower Rate of Genomic Mutations in Patients with Chronic Lymphocytic Leukemia.

To analyze the impact of the 11q deleted (11q-) cells in CLL patients on the time to first therapy (TFT) and overall survival (OS), 2,493 patients with CLL were studied. 242 patients (9.7%) had 11q-. Fluorescence in situ hybridization (FISH) studies showed a threshold of 40% of deleted cells to be optimal for showing that clinical differences in terms of TFT and OS within 11q- CLLs. In patients with ≥40% of losses in 11q (11q-H) (74%), the median TFT was 19 months compared with 44 months in CLL patients with <40% del(11q) (11q-L) (P<0.0001). In the multivariate analysis, only the presence of 11q-L, mutated IGHV status, early Binet stage and absence of extended lymphadenopathy were associated with longer TFT. Patients with 11q-H had an OS of 90 months, while in the 11q-L group the OS was not reached (P = 0.008). The absence of splenomegaly (P = 0.02), low LDH (P = 0.018) or ß2M (P = 0.006), and the presence of 11q-L (P = 0.003) were associated with a longer OS. In addition, to detect the presence of mutations in the ATM, TP53, NOTCH1, SF3B1, MYD88, FBXW7, XPO1 and BIRC3 genes, a select cohort of CLL patients with losses in 11q was sequenced by next-generation sequencing of amplicons. Eighty % of CLLs with 11q- showed mutations and fewer patients with low frequencies of 11q- had mutations among genes examined (50% vs 94.1%, P = 0.023). In summary, CLL patients with <40% of 11q- had a long TFT and OS that could be associated with the presence of fewer mutated genes.

Natural Enemies of the Frankliniella Complex Species (Thysanoptera: Thripidae) in Ataulfo Mango Agroecosystems.

A field survey was conducted in Ataulfo mango (Mangifera indica L.) orchards in Chiapas, Mexico, with the objective of determining the natural enemies of the Frankliniella complex species (Thysanoptera: Thripidae). Seven species of this genus feed and reproduce in large numbers during the mango flowering. Two representative orchards were selected: the orchard "Tres A" characterized by an intensive use of agrochemicals directed against thrips, and the orchard "La Escondida" that did not spray insecticides. During mango flowering, five inflorescences were randomly collected every 5 d in both orchards, for a total of 18 sampling dates. Results revealed the presence of 18 species of arthropods that were found predating on Frankliniella. There were 11 species in the families Aeolothripidae, Phlaeothripidae, Formicidae, Anthocoridae and Chrysopidae; and seven species of spiders in the families Araneidae, Tetragnathidae, and Uloboridae. Over 88% of predators were anthocorids, including, Paratriphleps sp. (Champion), Orius insidiosus (Say), Orius tristicolor (White), and O. perpunctatus (Reuter). The orchard that did not spray insecticides had a significantly higher number of predators suggesting a negative effect of the insecticides on the abundance of these organisms.