Comparison of DNA quantity and quality from fecal samples of mammals transported in ethanol or lysis buffer.

Using fecal microbial community profiles through sequencing approaches helps to unravel the intimate interplay between health, wellness, and diet in wild animals with their environment. Ensuring the proper preservation of fecal samples before processing is crucial to ensure reliable results. In this study, we evaluated the efficiency of two different preservation methods, considering the following criteria: DNA yield, quality and integrity, and microbial community structure based on Oxford Nanopore amplicon sequencing of the V3-V4 region of bacterial 16S rRNA and protozoa 18S rRNA genes. Eighteen matched pairs of mammalian fecal samples were collected and transported in 99.8% ethanol and lysis buffer; processing occurred between 55 and 461 days post-collection. Wilcoxon signed-rank tests were used to analyze quantitative measurements for paired samples. The A260/280 ratio, a measure of nucleic acid purity, was assessed descriptively for each media, and the Bartlett test evaluated dispersion of this ratio. A Fisher test was performed to compare the number of positive reactions for DNA extraction or PCR amplification of the 16S and 18S rRNA genes between both media. The concentration of total DNA and amplicons, as well as the number of reads obtained in sequencing, was significantly higher in the samples preserved with lysis buffer compared to ethanol, with magnitudes up to three times higher. Electrophoretic analysis of total DNA and amplicons further confirmed superior DNA integrity in lysis buffer preserved samples. The A260/280 values  obtained using the lysis buffer were of optimal purity (mean: 1.92) and with little dispersion (SD: 0.27); on the other hand, the ethanol samples also presented an excellent average quality (mean: 1.94), but they were dispersed (SD: 1.10). For molecular studies using mammalian feces, the lysis buffer reagent proved to be a reliable solution for their collection, conservation, and storage.

Pllans-II: Unveiling the Action Mechanism of a Promising Chemotherapeutic Agent Targeting Cervical Cancer Cell Adhesion and Survival Pathways.

Despite advances in chemotherapeutic drugs used against cervical cancer, available chemotherapy treatments adversely affect the patient's quality of life. For this reason, new molecules from natural sources with antitumor potential and few side effects are required. In previous research, Pllans-II, a phospholipase A2 type-Asp49 from Porthidium lansbergii lansbergii snake venom, has shown selective attack against the HeLa and Ca Ski cervical cancer cell lines. This work suggests that the cytotoxic effect generated by Pllans-II on HeLa cells is triggered without affecting the integrity of the cytoplasmic membrane or depolarizing the mitochondrial membranes. The results allow us to establish that cell death in HeLa is related to the junction blockage between α5ß1 integrins and fibronectin of the extracellular matrix. Pllans-II reduces the cells' ability of adhesion and affects survival and proliferation pathways mediated by intracellular communication with the external environment. Our findings confirmed Pllans-II as a potential prototype for developing a selective chemotherapeutic drug against cervical cancer.

New Y-SNPs in QM3 indigenous populations of Colombia.

In evolutionary studies of human populations based on the Y chromosome, the majority of Native Americans belong to the QM3 lineage. Therefore, to study the history of groups inhabiting northern South America, it is necessary to have a higher resolution of the tree. The objective of this work was to identify new SNPs of the QM3 lineage that would allow the evaluation of the phylogenetic relationships between Andean and Amazonian populations of Colombia. Sequences previously obtained from two Y chromosomes of Amazonian populations were used, from which 13 potential SNPs were selected and typed in 171 Amazonian samples from the Vaupés region and in 60 samples from the Pasto, Nasa, Embera, Arhuaco and Kogüi ethnic groups of the Andean region. In addition, the main SNPs/markers (L56, L54, M346, M848, Z780, CTS11780) defining autochthonous Q lineages were typed, along with others defined by different SNPs/markers as reported in the literature (CTS11357, SA05, Z19319, Z5915, and Z19384). It was found that all the new SNPs are present in the Amazonian samples and only 2 of them are shared with the Embera, Nasa and Pasto, but none with the Kogüi and Arhuaco from the northern Andes, in the Colombian Caribbean. Combining the 13 variants of the present study with 14 previously reported and using TMRCA, a new QM3 tree proposal is generated. This method makes it possible to increase the number of sublineages of QM3 with a higher resolution and to detect differences between the different populations of Vaupés in the Amazon, as in the case of the Kubeos and Pisamiras, the latter of which is in grave danger of extinction. These new sublineages are useful for microevolutionary studies of the Amerindian populations of South America.

PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2.

The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was -0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/.

Preliminary identification of pathogenic variants in an Afro-Colombian Raizal family with risk factors for glaucoma.

Objective: To identify pathogenic variants in an Afro-Colombian Raizal family with risk factors for glaucoma. Methods: In the present study, whole exome sequencing was performed on seven members of a Raizal family from the archipelago of San Andrés, Providencia, and Santa Catalina, in the Caribbean region of Colombia. Four of them had been diagnosed with glaucoma. In addition, two healthy volunteers from the island were included. Results: Of the 198 single nucleotide variants associated with glaucoma, previously reported by the DisGeNET database, four were identified in members of the Raizal family: rs11938093, rs7336216, rs3817672, and rs983034. Furthermore, single nucleotide variant rs983034 was identified in the Wnt ligand secretion mediator gene in all members of the family but not in healthy volunteers. Notably, WLS dysfunctions have been linked to pathology in the trabecular meshwork of the eye. Trabecular meshwork is an important regulator of the outflow of aqueous humor that maintains intraocular pressure (intraocular pressure) at normal levels. Damage to trabecular meshwork is associated with ocular hypertension, which leads to glaucoma progression. In relation to the other single nucleotide variants that were identified, their presence was confirmed in some members of the Raizal family. However, it is still unclear the pathophysiological cause that associates these single nucleotide variants with glaucoma. Conclusions: It was possible to identify four non-synonymous single nucleotide variants that predict significant damage to the structure and function of genes associated with glaucoma pathology in an Afro-Colombian.

Objetivo: Identificar las variantes patogénicas en una familia raizal afrocolombiana con factores de riesgo para el glaucoma. Métodos: En el presente estudio, se realizó una secuenciación de exoma completo en siete miembros de una familia Raizal del archipiélago de San Andrés, Providencia y Santa Catalina del Caribe colombiano. La mitad de ellos habían sido diagnosticados con glaucoma. Además, se incluyeron dos voluntarios sanos de la isla. Resultados: De las 198 variantes de un solo nucleótido (SNV) asociadas con el glaucoma, previamente informadas por la base de datos DisGeNET, se identificaron cuatro en los miembros de la familia Raizal: rs11938093, rs7336216, rs3817672 y rs983034. Ademas, en todos los miembros de la familia, pero no en voluntarios sanos, se identificó SNV rs983034 en el gen mediador de secreción de ligando Wnt (WLS). Notablemente, las disfunciones WLS se han relacionado con patologías en la red trabecular (TM) del ojo. TM es un regulador importante del flujo de salida del humor acuoso que mantiene la presión intraocular (presión intraocular) en niveles normales. El daño a la TM se asocia con hipertensión ocular que conduce a la progresión del glaucoma. En relación con los demás SNV identificados, se constató su presencia en algunos miembros de la familia Raizal. Sin embargo, aún no está clara la causa fisiopatológica que asocia estas SNV con el glaucoma. Conclusiones: Fue posible identificar cuatro SNVs no sinónimos con predicción de daño significativo en la estructura y función de genes asociados a patología de glaucoma en un afrocolombiano.

Pllans-II Induces Cell Death in Cervical Cancer Squamous Epithelial Cells via Unfolded Protein Accumulation and Endoplasmic Reticulum Stress.

Due to the lack of chemotherapeutic drugs that selectively affect cervical cancer cells, natural sources such as snake venom are currently being investigated for molecules with antitumor potential. Pllans-II, a phospholipase A2 type-Asp49 from Porthidium lansbergii lansbergii snake venom, induced cell death in a cervical cancer cell line-Ca Ski-related to dysfunction in the ability to resolve endoplasmic reticulum stress, evidenced by sub-expression of genes such as PERK, ERO1 PDIs, HSP70, and CHOP. Western blot analysis validated the last two genes' sub-expression at the protein level. In addition, Pllans-II presented a dose-dependent cytotoxic effect on cancer cells and an insignificant effect on healthy endothelial cells (HUVEC). Additionally, Pllans-II inhibited cancer cells' adhesion and migration capacity, induced cell cycle arrest in the G2/M phase, and induced apoptosis stimulated possibly by the extrinsic route. These results demonstrate for the first time that Pllans-II has an antitumor effect on a squamous epithelial cervical cancer cell line and represents a possible biotechnological tool for designing a prominent antitumor agent.

Preliminary identification of pathogenic variants in an Afro-Colombian Raizal family with risk factors for glaucoma / Identificación preliminar de variantes patógenas en una familia raizal afrocolombiana con factores de riesgo para glaucoma

Abstract Objective: To identify pathogenic variants in an Afro-Colombian Raizal family with risk factors for glaucoma. Methods: In the present study, whole exome sequencing was performed on seven members of a Raizal family from the archipelago of San Andrés, Providencia, and Santa Catalina, in the Caribbean region of Colombia. Four of them had been diagnosed with glaucoma. In addition, two healthy volunteers from the island were included. Results: Of the 198 single nucleotide variants associated with glaucoma, previously reported by the DisGeNET database, four were identified in members of the Raizal family: rs11938093, rs7336216, rs3817672, and rs983034. Furthermore, single nucleotide variant rs983034 was identified in the Wnt ligand secretion mediator gene in all members of the family but not in healthy volunteers. Notably, WLS dysfunctions have been linked to pathology in the trabecular meshwork of the eye. Trabecular meshwork is an important regulator of the outflow of aqueous humor that maintains intraocular pressure (intraocular pressure) at normal levels. Damage to trabecular meshwork is associated with ocular hypertension, which leads to glaucoma progression. In relation to the other single nucleotide variants that were identified, their presence was confirmed in some members of the Raizal family. However, it is still unclear the pathophysiological cause that associates these single nucleotide variants with glaucoma. Conclusions: It was possible to identify four non-synonymous single nucleotide variants that predict significant damage to the structure and function of genes associated with glaucoma pathology in an Afro-Colombian.

Resumen Objetivo: Identificar las variantes patogénicas en una familia raizal afrocolombiana con factores de riesgo para el glaucoma. Métodos: En el presente estudio, se realizó una secuenciación de exoma completo en siete miembros de una familia Raizal del archipiélago de San Andrés, Providencia y Santa Catalina del Caribe colombiano. La mitad de ellos habían sido diagnosticados con glaucoma. Además, se incluyeron dos voluntarios sanos de la isla. Resultados: De las 198 variantes de un solo nucleótido (SNV) asociadas con el glaucoma, previamente informadas por la base de datos DisGeNET, se identificaron cuatro en los miembros de la familia Raizal: rs11938093, rs7336216, rs3817672 y rs983034. Ademas, en todos los miembros de la familia, pero no en voluntarios sanos, se identificó SNV rs983034 en el gen mediador de secreción de ligando Wnt (WLS). Notablemente, las disfunciones WLS se han relacionado con patologías en la red trabecular (TM) del ojo. TM es un regulador importante del flujo de salida del humor acuoso que mantiene la presión intraocular (presión intraocular) en niveles normales. El daño a la TM se asocia con hipertensión ocular que conduce a la progresión del glaucoma. En relación con los demás SNV identificados, se constató su presencia en algunos miembros de la familia Raizal. Sin embargo, aún no está clara la causa fisiopatológica que asocia estas SNV con el glaucoma. Conclusiones: Fue posible identificar cuatro SNVs no sinónimos con predicción de daño significativo en la estructura y función de genes asociados a patología de glaucoma en un afrocolombiano.

Novel mutations in breast cancer patients from southwestern Colombia.

Breast cancer is the leading cause of death by cancer among women in less developed regions. In Colombia, few published studies have applied next-generation sequencing technologies to evaluate the genetic factors related to breast cancer. This study characterized the exome of three patients with breast cancer from southwestern Colombia to identify likely pathogenic or disease-related DNA sequence variants in tumor cells. For this, the exomes of three tumor tissue samples from patients with breast cancer were sequenced. The bioinformatics analysis identified two pathogenic variants in Fgfr4 and Nf1 genes, which are highly relevant for this type of cancer. Specifically, variant FGFR4-c.1162G>A predisposes individuals to a significantly accelerated progression of this pathology, while NF1-c.1915C>T negatively alters the encoded protein and should be further investigated to clarify the role of this variant in this neoplasia. Moreover, 27 novel likely pathogenic variants were found and 10 genes showed alterations of pathological interest. These results suggest that the novel variants reported here should be further studied to elucidate their role in breast cancer.

Identifying new lineages in the Y chromosome of Colombian Amazon indigenous populations.

OBJECTIVES: The Y chromosome has highly informative markers, such as single-nucleotide polymorphisms (SNPs), that are useful for making historical inferences about the settlement of the Americas. However, the scarcity of these markers has limited their use. This study aims to identify new SNPs and increase the phylogenetic resolution of haplogroup Q for the Americas, mainly focusing on the lineages of the Amazon region. MATERIALS AND METHODS: Next-generation sequencing was performed on two Y chromosomes belonging to haplogroup Q-M3 using samples with divergent short tandem repeat haplotypes from the Colombian Amazon, and 14 of the new variants identified were selected for characterization in 207 samples of indigenous Colombians belonging to haplogroup Q-M3. RESULTS: This methodology allowed us to establish nine new lineages within Q-M3, including its paragroups. The most basal lineages were predominant in communities of Andean origin, such as the Embera-Katio, the Nasas, and the Pastos. In contrast, the most distal lineages were restricted to inhabitants of the Amazon region of Vaupés. DISCUSSION: The SNPs reported here advance the development of subhaplogroups of Q-M3 with a higher level of phylogenetic resolution than has been previously reported, which allowed the differentiation between populations that inhabit two regions of Vaupes area: the Pirá-Paraná region and the upper and middle sections of the Vaupés River, and the region encompassing the Papurí River and the lower Vaupés. They are very useful for the microevolutionary analysis of the Amerindian populations of Colombia and of the Americas.

Hallux valgus: comparative study between two surgical techniques of proximal addition osteotomy.

OBJECTIVE: TO CLINICALLY AND RADIOGRAPHICALLY COMPARE THE RESULTS OF TREATMENT OF HALLUX VALGUS, BY TWO ADDITION OSTEOTOMY TECHNIQUES: one using resected exostosis, and the other using a plate fixation for addition wedge. METHODS: We evaluated 24 feet of 19 patients, mean age 51.3 years, affected by hallux valgus, with a mean follow-up of 50.1 months. 13 feet underwent addition osteotomy with resected exostosis (AORE) and 11 patients (11 feet) underwent addition osteotomy with plate (AOP). The AOFAS score, intermetatarsal 1 and 2 angles, and hallux valgus angle were evaluated before and after surgery. RESULTS: In the AORE technique, the mean preoperative AOFAS was 46.6, with IMA 14(o) and HVA 32o, while in the postoperative AOFAS it was 81.3, with IMA 9(o) and HVA 25(o), and 92.3% satisfactory results. In the AOP technique, the mean preoperative AOFAS was 42.1, with IMA 15(o) and HVA 29(o) while in the postoperative AOFAS it was 77.4, with IMA 11(o) and HVA 23(o) and 81.8% of satisfactory results. CONCLUSIONS: Both techniques proved to be effective in the treatment of hallux valgus, both clinically and radiografically, with no statistical difference between them. Level of evidence III, Retrospective comparative study.

Effect of combined nicotine and shrapnel exposure on pain measures and gait after nerve injury.

A significant fraction of military soldiers sustain nerve injury and use tobacco or nicotine containing products. Healing of nerve injuries is influenced by many factors, such as degree of original injury, healing potential of the nerve, and general health of patient. However, recently, it has been demonstrated that the presence of retained insoluble metal fragments decreases healing. The effects of systemic nicotine administration, with or without metal fragments at the site of nerve injury, were evaluated. Both the nicotine-administered groups (nicotine, nicotine + shrapnel) showed significant increase in the peroneal function compared with untreated controls, as assessed by paw area (p < 0.05). Furthermore, to test possible role of altered sensory function, we used the hot plate assay. Latency to withdraw paw from a hot plate was significantly shorter in nicotine groups (p < 0.05). These data indicate that nicotine improves sensory and motor aspects of nerve function, in the presence or absence of shrapnel.

Role of growth factors in improved skin flap viability caused by phosphodiesterase-5 inhibitor.

Flap necrosis is one of the major complications of reconstructive surgery and sildenafil citrate has been shown to decrease flap necrosis in preclinical animal models. However, the mechanisms underlying sildenafil's therapeutic efficacy are not known. As with other phosphodiesterase 5 selective inhibitors, sildenafil causes vasodilation and enhanced blood flow. In addition, sildenafil can also alter gene expression. This study is designed to test the hypothesis that increased expression of angiogenic growth factors may be responsible for therapeutic efficacy of sildenafil. A modified McFarlane flap measuring 3 x 10 cm was created on the dorsal skin of male Sprague-Dawley rats. For growth factor expression experiment, rats were administered either vehicle or sildenafil 10 mg/Kg intraperitoneal (IP). Ribonucleic acid (RNA) extracted from skin flap was analyzed to assess the messenger ribonucleic acid (mRNA) levels of different angiogenic growth factors. For skin flap viability experiment, fibrin film impregnated with vehicle, fibroblast growth factor (FGF) (5.0 microg) or vascular endothelial growth factor (VEGF) (2.0 microg) was applied to the wound. The skin flap was then returned to its native position and stapled in place. Total affected area (area of necrosis and blood flow stasis) of each rat on postoperative day 14 was analyzed with orthogonal polarization spectral imaging. Daily systemic treatment with sildenafil significantly (P < 0.05) increased the expression of FGF1 and FGF Receptor 3 on postoperative day 3 by 5.08- and 4.78-fold, respectively. In addition, sildenafil increased the expression of VEGF-A, VEGF-B, and VEGF-C by 2.66-, 2.02-, and 2.00-fold, respectively. Subcutaneous treatment with FGF but not VEGF-A tended to decrease total affected area in rats. These data demonstrate that sildenafil altered the expression of FGF and VEGF. Altered expression of growth factors may be, at least partly, responsible for the beneficial effects of sildenafil citrate on skin viability.

Design and implementation of dynamic near-infrared optical tomographic imaging instrumentation for simultaneous dual-breast measurements.

Dynamic near-infrared optical tomographic measurement instrumentation capable of simultaneous bilateral breast imaging, having a capability of four source wavelengths and 32 source-detector fibers for each breast, is described. The system records dynamic optical data simultaneously from both breasts, while verifying proper optical fiber contact with the tissue through implementation of automatic schemes for evaluating data integrity. Factors influencing system complexity and performance are discussed, and experimental measurements are provided to demonstrate the repeatability of the instrumentation. Considerations in experimental design are presented, as well as techniques for avoiding undesirable measurement artifacts, given the high sensitivity and dynamic range (1:10(9)) of the system. We present exemplary clinical results comparing the measured physiologic response of a healthy individual and of a subject with breast cancer to a Valsalva maneuver.