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1.
Glob Chang Biol ; 30(3): e17229, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38511643

RESUMEN

A clear definition of carbon sequestration in soils is necessary to quantify soil's role in climate change mitigation accurately. Don et al. (2023) proposed defining carbon sequestration as "[the] Process of transferring carbon from the atmosphere into the soil through plants or other organisms, which is retained as soil organic carbon resulting in a global carbon stock increase of the soil". In our view, this definition is incomplete because a comprehensive definition of carbon sequestration should explicitly include the time that carbon remains stored in an ecosystem, thus mitigating its contribution to the greenhouse effect.


Asunto(s)
Ecosistema , Suelo , Secuestro de Carbono , Carbono , Cambio Climático
2.
J Sci Food Agric ; 2023 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-37872724

RESUMEN

Roots, tubers and bananas (RTBs) contribute immensely to food security and livelihoods in sub-Saharan Africa, Asia and Latin America. The adoption of RTB genotypes in these regions relies on the interplay among agronomic traits, ease of processing and consumer preference. In breeding RTBs, until recently little attention was accorded key textural traits preferred by consumers. Moreover, a lack of standard, discriminant, repeatable protocols that can be used to measure the textural traits deter linkages between breeding better RTB genotypes and end user/consumer preferences. RTB products texture - that is, behaviour of RTB food products under unique deformations, such as disintegration and the flow of a food under force - is a critical component of these preferences. The preferences consumers have for certain product texture can be evaluated from expert sensory panel and consumer surveys, which are useful tools in setting thresholds for textural traits, and inform breeders on what to improve in the quality of RTBs. Textural characterization of RTBs under standard operating procedures (SOPs) is important in ensuring the standardization of texture measurement conditions, predictability of textural quality of RTBs, and ultimately definition of RTB food product profiles. This paper reviews current SOPs for the textural characterization of RTBs, including their various associated methods, parameters, challenges and merits. Case studies of texture characterized during development of SOPs and evaluation of texture of RTB populations are discussed, together with insights into key textural attributes and correlations between instrumental, sensory and consumer assessment of texture unique to various RTB food products. Hardness was considered a universal key textural attribute to discriminate RTBs. The review should provide adequate insight into texture of RTB food products and critical factors in their measurement. It aims to promote inclusion of texture in breeding pipelines by investigating which textural traits are prioritized by consumers, particularly since the inclusion of textural traits has recently gained prominence by breeders in improving RTBs. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

3.
Support Care Cancer ; 30(10): 8547-8557, 2022 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-35579752

RESUMEN

Cancer patients have an increased risk of bleeding compared to non-cancer patients with anticoagulant therapy. A bleeding risk assessment before initiation of anticoagulation is recommended. Currently low molecular weight heparin (LMWH) and direct oral anticoagulants (DOACs) are the mainstays of treatment for cancer-associated venous thromboembolism (VTE). Since DOACs are administered orally, they offer some convenience and ease of administration; however, LMWH may be preferred in certain cancers. Given the prevalence of anticoagulant therapies in cancer patients, clinical providers must be able to recognize potentially critical bleeding sites and modalities to reverse major hemorrhage. Reversal agents or antidotes to bleeding may be required when bleeding is persistent or life-threatening. These include vitamin K, fresh frozen plasma (FFP), protamine, prothrombin complex concentrate (PCC) or andexanet alfa, and idarucizumab. Inferior vena cava (IVC) filter insertion can be also considered in those with major bleeding. Evidence for timing and need for re-initiation of anticoagulant therapy after a major bleeding remains sparse, but a multi-disciplinary approach and shared decision-making can be implemented in the interim.


Asunto(s)
Heparina de Bajo-Peso-Molecular , Neoplasias , Administración Oral , Anticoagulantes/efectos adversos , Antídotos/uso terapéutico , Hemorragia/inducido químicamente , Hemorragia/prevención & control , Heparina de Bajo-Peso-Molecular/uso terapéutico , Humanos , Neoplasias/complicaciones , Neoplasias/tratamiento farmacológico , Protaminas/uso terapéutico , Vitamina K
4.
Can J Microbiol ; 67(10): 749-770, 2021 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-34237221

RESUMEN

The last two decades have seen vigorous activity in synthetic biology research and the ever-increasing applications of these technologies. However, pedagogical research pertaining to teaching synthetic biology is scarce, especially when compared to other science and engineering disciplines. Within Canada, there are only three universities that offer synthetic biology programs, two of which are at the undergraduate level. Rather than taking place in formal academic settings, many Canadian undergraduate students are introduced to synthetic biology through participation in the annual International Genetically Engineered Machine (iGEM) competition. Although the iGEM competition has had a transformative impact on synthetic biology training in other nations, its impact in Canada has been relatively modest. Consequently, the iGEM competition remains a major setting for synthetic biology education in Canada. To promote further development of synthetic biology education, we surveyed undergraduate students from the Canadian iGEM design teams of 2019. We extracted insights from these data using qualitative analysis to provide recommendations for best teaching practices in synthetic biology undergraduate education, which we describe through our proposed Framework for Transdisciplinary Synthetic Biology Education (FTSBE).


Asunto(s)
Ingeniería Genética , Biología Sintética , Canadá , Humanos , Estudiantes , Universidades
5.
Nanotechnology ; 29(33): 332001, 2018 Aug 17.
Artículo en Inglés | MEDLINE | ID: mdl-29794338

RESUMEN

Cancer has become the most prevalent cause of deaths, placing a huge economic and healthcare burden worldwide. Nanoparticles (NPs), as a key component of nanomedicine, provide alternative options for promoting the efficacy of cancer therapy. Current conventional cancer models have limitations in predicting the effects of various cancer treatments. To overcome these limitations, biomimetic and novel 'tumor-on-a-chip' platforms have emerged with other innovative biomedical engineering methods that enable the evaluation of NP-based cancer therapy. In this review, we first describe cancer models for evaluation of NP-based cancer therapy techniques, and then present the latest advances in 'tumor-on-a-chip' platforms that can potentially facilitate clinical translation of NP-based cancer therapies.


Asunto(s)
Ingeniería Biomédica/métodos , Dispositivos Laboratorio en un Chip , Modelos Biológicos , Nanomedicina/métodos , Nanopartículas/uso terapéutico , Neoplasias/terapia , Animales , Antineoplásicos/farmacología , Ingeniería Biomédica/instrumentación , Técnicas de Cultivo de Célula , Línea Celular Tumoral , Modelos Animales de Enfermedad , Rayos gamma/uso terapéutico , Humanos , Hipertermia Inducida/métodos , Ratones , Nanomedicina/instrumentación , Neoplasias/patología , Esferoides Celulares/efectos de los fármacos , Esferoides Celulares/patología , Esferoides Celulares/efectos de la radiación , Ensayos Antitumor por Modelo de Xenoinjerto
7.
Rev Gastroenterol Peru ; 34(3): 229-35, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25293992

RESUMEN

Barrett's esophagus is a distal metaplasia characterized by the transformation of squamous mucosa into columnar mucosa. This esophageal phenotype is a product not only of the chronic reflux of gastric acids, but also by microorganisms that colonize the oral cavity and stomach. Two classes of microbiota can be identified in Barrett's esophagus; microbiota type I is associated with the normal esophagus and type II with an inflamed esophagus. The present study describes the gastric microbiota of a patient with antral gastritis concomitant with Barrett's esophagus absent infection with Helicobacter pylori. Gastric biopsies were obtained following the protocol of Sydney and following ethical practices. The isolates were cultivated under microaerophilic conditions on Columbia Agar supplemented with IsoVitaleX™ and 7% sterile blood. Extracted DNA was sequenced using 454-GS and the results analyzed on the MG-RAST server. Gram negative isolates were found and bacteria resistant to levofloxacin, amoxicillin, tetracycline, erythromycin, and clarithromycin. The phyla Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, the genus Bacteroides and the species group Bacteroides fragilis were most abundant. Functionally, the metabolism of carbohydrates, amino acids, and to a lesser extent, the metabolism of cofactors and vitamins were most dominant, and of which the enzymes ß-glucosidase (EC 3.2.1.21), ß-galactosidase (EC 3.2.1.23) and ß-N-acetylhexosaminidase (EC 3.2.1.52) were most dominant. The findings of this study, because they are of only one case may probably suggest a possible pathogenic role, previously undescribed for Bacteroides fragilis, associated with human gastritis when concomitant esophageal pathology exists.


Asunto(s)
Esófago de Barrett/microbiología , Gastritis/microbiología , Microbioma Gastrointestinal/genética , Metagenómica , Estómago/microbiología , Esófago de Barrett/complicaciones , Femenino , Gastritis/complicaciones , Humanos , Persona de Mediana Edad
8.
Cureus ; 16(3): e57055, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38681263

RESUMEN

As our understanding of the intricate interaction between gut bacteria and human health continues to expand, so too has interest in the ability of probiotics to manage gut microbiota and confer multiple health benefits to the host. The mini literature review focuses on the expanding potential of the use of probiotics in GI health, with a focus on probiotics' potential therapeutic advantages in a variety of gastrointestinal (GI) illnesses. Probiotics play a significant role in managing diarrhea and symptoms of irritable bowel syndrome with diarrhea (IBS-D) by modulating gut microbial communities. Specific probiotic strains have been found to reduce the abundance of harmful bacteria, regulate inflammatory markers like interleukin 6, and improve GI symptoms such as abdominal discomfort and stool consistency. Additionally, probiotic blends have shown potential for preventing GI infections and alleviating GI pain in IBS-D patients. Studies have demonstrated that certain multi-strain probiotics, including Bifidobacterium and Lactobacillus species, can significantly increase the frequency of bowel movements and reduce the proportion of individuals experiencing constipation. It has also been found that probiotic supplementation may reduce the incidence of postoperative complications and mortality, particularly in patients undergoing colorectal adenocarcinoma surgery. Additionally, probiotics have been associated with decreased levels of pro-inflammatory cytokines and improved clinical outcomes in patients with colorectal cancer. Furthermore, probiotics have been associated with enhanced digestive tolerance, reduced GI inflammation, and prolonged clinical remission in certain UC patients. Studies have also shown that probiotics, administered either directly to infants or pregnant women during the perinatal stage, can alleviate symptoms such as inconsolable crying and irritation associated with infant colic, improve bowel movement frequency in cases of functional constipation, and enhance overall conditions in premature infants, including reducing regurgitation and improving feeding tolerance. The review addresses both encouraging results and challenges with probiotic therapy, while also arguing for more studies to elucidate underlying mechanisms and enhance therapeutic techniques. As we traverse the complex field of probiotic therapy in the treatment of GI illnesses, researchers, physicians, and other healthcare professionals can benefit from the informative information provided by this study.

9.
Micromachines (Basel) ; 14(5)2023 Apr 28.
Artículo en Inglés | MEDLINE | ID: mdl-37241590

RESUMEN

The eutrophication of aquatic ecosystems caused by rapid human urbanization has led to an increased production of potentially hazardous bacterial populations, known as blooms. One of the most notorious forms of these aquatic blooms are cyanobacteria, which in sufficiently large quantities can pose a hazard to human health through ingestion or prolonged exposure. Currently, one of the greatest difficulties in regulating and monitoring these potential hazards is the early detection of cyanobacterial blooms, in real time. Therefore, this paper presents an integrated microflow cytometry platform for label-free phycocyanin fluorescence detection, which can be used for the rapid quantification of low-level cyanobacteria and provide early warning alerts for potential harmful cyanobacterial blooms. An automated cyanobacterial concentration and recovery system (ACCRS) was developed and optimized to reduce the assay volume, from 1000 mL to 1 mL, to act as a pre-concentrator and subsequently enhance the detection limit. The microflow cytometry platform utilizes an on-chip laser-facilitated detection to measure the in vivo fluorescence emitted from each individual cyanobacterial cell, as opposed to measuring overall fluorescence of the whole sample, potentially decreasing the detection limit. By applying transit time and amplitude thresholds, the proposed cyanobacteria detection method was verified by the traditional cell counting technique using a hemocytometer with an R2 value of 0.993. It was shown that the limit of quantification of this microflow cytometry platform can be as low as 5 cells/mL for Microcystis aeruginosa, 400-fold lower than the Alert Level 1 (2000 cells/mL) set by the World Health Organization (WHO). Furthermore, the decreased detection limit may facilitate the future characterization of cyanobacterial bloom formation to better provide authorities with ample time to take the appropriate actions to mitigate human risk from these potentially hazardous blooms.

10.
Biosensors (Basel) ; 13(10)2023 Oct 18.
Artículo en Inglés | MEDLINE | ID: mdl-37887128

RESUMEN

The global economic and healthcare crises experienced over the past three years, as a result of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted the commonplace habits of humans around the world. SARS-CoV-2, the virus responsible for the coronavirus 2019 (COVID-19) phenomenon, has contributed to the deaths of millions of people around the world. The potential diagnostic applications of microfluidic devices have previously been demonstrated to effectively detect and quasi-quantify several different well-known viruses such as human immunodeficiency virus (HIV), influenza, and SARS-CoV-2. As a result, microfluidics has been further explored as a potential alternative to our currently available rapid tests for highly virulent diseases to better combat and manage future potential outbreaks. The outbreak management during COVID-19 was initially hindered, in part, by the lack of available quantitative rapid tests capable of confirming a person's active infectiousness status. Therefore, this review will explore the use of microfluidic technology, and more specifically RNA-based virus detection methods, as an integral part of improved diagnostic capabilities and will present methods for carrying the lessons learned from COVID-19 forward, toward improved diagnostic outcomes for future pandemic-level threats. This review will first explore the context of the COVID-19 pandemic and how diagnostic technology was shown to have required even greater advancements to keep pace with the transmission of such a highly infectious virus. Secondly, the historical significance of integrating microfluidic technology in diagnostics and how the different types of genetic-based detection methods may vary in their potential practical applications. Lastly, the review will summarize the past, present, and future potential of RNA-based virus detection/diagnosis and how it might be used to better prepare for a future pandemic.


Asunto(s)
COVID-19 , SARS-CoV-2 , Humanos , COVID-19/diagnóstico , Pandemias , Prueba de COVID-19 , ARN
11.
Bioengineering (Basel) ; 10(7)2023 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-37508864

RESUMEN

Acupuncture is one of the most extensively used complementary and alternative medicine therapies worldwide. In this study, we explore the use of near-infrared light-emitting diodes (LEDs) to provide acupuncture-like physical stimulus to the skin tissue, but in a completely non-invasive way. A computational modeling framework has been developed to investigate the light-tissue interaction within a three-dimensional multi-layer model of skin tissue. Finite element-based analysis has been conducted, to obtain the spatiotemporal temperature distribution within the skin tissue, by solving Pennes' bioheat transfer equation, coupled with the Beer-Lambert law. The irradiation profile of the LED has been experimentally characterized and imposed in the numerical model. The experimental validation of the developed model has been conducted through comparing the numerical model predictions with those obtained experimentally on the agar phantom. The effects of the LED power, treatment duration, LED distance from the skin surface, and usage of multiple LEDs on the temperature distribution attained within the skin tissue have been systematically investigated, highlighting the safe operating power of the selected LEDs. The presented information about the spatiotemporal temperature distribution, and critical factors affecting it, would assist in better optimizing the desired thermal dosage, thereby enabling a safe and effective LED-based photothermal therapy.

12.
JMIR Res Protoc ; 12: e37442, 2023 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-35759752

RESUMEN

BACKGROUND: Core outcome sets (COSs) are important and necessary as they help standardize reporting in research studies. Cranioplasty following traumatic brain injury (TBI) or stroke is becoming increasingly common, leading to an ever-growing clinical and research interest, especially regarding the optimal material, cost-effectiveness, and timing of cranioplasty concerning neurological recovery and complications. Consequently, heterogeneous reporting of outcomes from such diverse studies has led to limited meta-analysis ability and an ongoing risk of outcome reporting bias. This study aims to define a standardized COS for reporting in all future TBI and stroke cranioplasty studies. OBJECTIVE: This study has four aims: (1) undertake a systematic review to collate the most current outcome measures used within the cranioplasty literature; (2) undertake a qualitative study to understand better the views of clinicians, patients' relatives, and allied health professionals regarding clinical outcomes following cranioplasty; (3) undertake a Delphi survey as part of the process of gaining consensus for the COS; and (4) finalize consensus through a consensus meeting resulting in the COS. METHODS: An international steering committee has been formed to guide the development of the COS. In addition, recommendations from other clinical initiatives such as COMET (Core Outcomes and Effectiveness Trials) and OMERACT (Outcome Measures in Rheumatology) have been adhered to. Phase 1 is data collection through a systematic review and qualitative study. Phase 2 is the COS development through a Delphi survey and consensus meetings with consensus definitions decided and agreed upon before the Delphi survey begins to avoid bias. RESULTS: Phase 1 started at the end of 2019, following ethical approval in December 2019, and the project completion date is planned for the end of 2022 or beginning of 2023. CONCLUSIONS: This study should result in a consensus on a COS for cranioplasty, following TBI or stroke, to help standardize outcome reporting for future studies, which can be applied to future research and clinical services, help align future studies, build an increased understanding of cranioplasty and its impact on a patient's function and recovery, and help standardize the evidence base. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/37442.

13.
Micromachines (Basel) ; 12(9)2021 Sep 07.
Artículo en Inglés | MEDLINE | ID: mdl-34577722

RESUMEN

The rapid detection and quantification of infectious pathogens is an essential component to the control of potentially lethal outbreaks among human populations worldwide. Several of these highly infectious pathogens, such as Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have been cemented in human history as causing epidemics or pandemics due to their lethality and contagiousness. SARS-CoV-2 is an example of these highly infectious pathogens that have recently become one of the leading causes of globally reported deaths, creating one of the worst economic downturns and health crises in the last century. As a result, the necessity for highly accurate and increasingly rapid on-site diagnostic platforms for highly infectious pathogens, such as SARS-CoV-2, has grown dramatically over the last two years. Current conventional non-microfluidic diagnostic techniques have limitations in their effectiveness as on-site devices due to their large turnaround times, operational costs and the need for laboratory equipment. In this review, we first present criteria, both novel and previously determined, as a foundation for the development of effective and viable on-site microfluidic diagnostic platforms for several notable pathogens, including SARS-CoV-2. This list of criteria includes standards that were set out by the WHO, as well as our own "seven pillars" for effective microfluidic integration. We then evaluate the use of microfluidic integration to improve upon currently, and previously, existing platforms for the detection of infectious pathogens. Finally, we discuss a stage-wise means to translate our findings into a fundamental framework towards the development of more effective on-site SARS-CoV-2 microfluidic-integrated platforms that may facilitate future pandemic diagnostic and research endeavors. Through microfluidic integration, many limitations in currently existing infectious pathogen diagnostic platforms can be eliminated or improved upon.

14.
Int J Food Sci Technol ; 56(3): 1193-1205, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33776230

RESUMEN

Consumers prefer cassava roots that cook quickly during boiling. Current methods to evaluate cooking time (CT) are slow and labour-intensive. This article describes improved protocols for assessing CT in roots. We evaluated CT in 36 genotypes monthly at 8-11 months after planting. CT showed differences for plant age at harvest and among genotypes. During boiling, roots absorbed water (WAB) and thus reduced their relative density (DEN). We classified three groups of genotypes with increasing CT (≤25 min, 25-40 min and >40 min), associated with decreasing WAB, respectively, 15.3 ± 3.1, 10.7 ± 1.7 and 4.9 ± 3.8% of initial root weight. A similar trend was observed for changes in DEN (46.3 ± 9.8, 54.5 ± 11.1 and 75.9 ± 6.9% of initial DEN, respectively). The highest correlations between WAB and DEN with CT (r 2 > 0.6) were found at 30-min boiling. These alternative protocols facilitate screening large numbers of cassava genotypes for CT.

15.
Int J Food Sci Technol ; 56(3): 1298-1310, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33776237

RESUMEN

Gari is a common cassava precooked dried semolina in sub-Saharan Africa. Our study investigated the role of process parameters and mash water content on gari quality during traditional roasting stage. The statistical analysis for eight quality criteria revealed that gari quality is highly influenced by the process parameters adopted by the operators. To emphasise the twin impact of roasting parameters and mash water content, different mashes with varying water content were roasted leading to different adjustments of the roasting conditions according to the operators. When the variability of the water content becomes greater, a greater variability in the final quality of the obtained garis was observed between operators (lightness, swelling capacity, starch content, texture and colour). These results suggest that technological improvements to the gari process could be achieved by appropriate management of the roasting and dewatering parameters.

16.
Int J Food Sci Technol ; 56(3): 1311-1321, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33776238

RESUMEN

The gari-making process involves several unit operations (U.O.), some of which strongly influence the quality of the end product. Two contrasting process scales (laboratory-scale vs conventional) were compared in order to identify which U.O. were affected by the change of scale. U.O. that changed end-product characteristics depending on process scale were deemed critical; whereas U.O. that resulted in similar characteristics were deemed robust. The classification depended on quality attributes considered: rasping and roasting were critical for physical properties, in particular particle size which ranged from 0.44 to 0.89 mm between the two process scales; and robust for biochemical properties. In contrast, fermentation and pressing were critical for biochemical properties such as lactic acid content (0.93-1.88 g/100 g dry matter after pressing), which influences the perception of flavour, and robust for physical properties. This classification between critical and robust operations help quality control of gari, by pinpointing which U.O. control specific quality characteristics.

17.
Cell Rep ; 32(11): 108159, 2020 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-32937132

RESUMEN

Helicobacter pylori (Hp) is an important human pathogen associated with gastric inflammation and neoplasia. It is commonly believed that this bacterium avoids major immune recognition by Toll-like receptors (TLRs) because of low intrinsic activity of its flagellin and lipopolysaccharides (LPS). In particular, TLR5 specifically detects flagellins in various bacterial pathogens, while Hp evolved mutations in flagellin to evade detection through TLR5. Cancerogenic Hp strains encode a type IV secretion system (T4SS). The T4SS core component and pilus-associated protein CagY, a large VirB10 ortholog, drives effector molecule translocation. Here, we identify CagY as a flagellin-independent TLR5 agonist. We detect five TLR5 interaction sites, promoting binding of CagY-positive Hp to TLR5-expressing cells, TLR5 stimulation, and intracellular signal transduction. Consequently, CagY constitutes a remarkable VirB10 member detected by TLR5, driving crucial innate immune responses by this human pathogen.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Helicobacter pylori/metabolismo , Secuencias Repetitivas de Aminoácido , Receptor Toll-Like 5/metabolismo , Animales , Sitios de Unión , Secuencia Conservada , Mucosa Gástrica/metabolismo , Mucosa Gástrica/microbiología , Mucosa Gástrica/patología , Células HEK293 , Humanos , Modelos Biológicos , Mutagénesis/genética , Péptidos/metabolismo , Dominios Proteicos , Gastropatías/microbiología , Gastropatías/patología , Relación Estructura-Actividad , Receptor Toll-Like 5/agonistas , Receptor Toll-Like 5/genética , Regulación hacia Arriba/genética , Pez Cebra
18.
Front Microbiol ; 11: 601839, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33381095

RESUMEN

Region-specific Helicobacter pylori subpopulations have been identified. It is proposed that the hspAmerind subpopulation is being displaced from the Americans by an hpEurope population following the conquest. Our study aimed to describe the genomes and methylomes of H. pylori isolates from distinct Peruvian communities: 23 strains collected from three groups of Native Americans (Asháninkas [ASHA, n = 9], Shimaas [SHIM, n = 5] from Amazonas, and Punos from the Andean highlands [PUNO, n = 9]) and 9 modern mestizos from Lima (LIM). Closed genomes and DNA modification calls were obtained using SMRT/PacBio sequencing. We performed evolutionary analyses and evaluated genomic/epigenomic differences among strain groups. We also evaluated human genome-wide data from 74 individuals from the selected Native communities (including the 23 H. pylori strains donors) to compare host and bacterial backgrounds. There were varying degrees of hspAmerind ancestry in all strains, ranging from 7% in LIM to 99% in SHIM. We identified three H. pylori subpopulations corresponding to each of the Native groups and a novel hspEuropePeru which evolved in the modern mestizos. The divergence of the indigenous H. pylori strains recapitulated the genetic structure of Native Americans. Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence. The prevalence of cagA +/vacA s1i1m1 genotype was similar across populations (p = 0.32): 89% in ASHA, 67% in PUNO, 56% in LIM and 40% in SHIM. Both cagA and vacA sequences showed that LIM strains were genetically differentiated (p < 0.001) as compared to indigenous strains. We identified 642 R-M systems with 39% of the associated genes located in the core genome. We found 692 methylation motifs, including 254 population-specific sequences not previously described. In Peru, hspAmerind is not extinct, with traces found even in a heavily admixed mestizo population. Notably, our study identified three new hspAmerind subpopulations, one per Native group; and a new subpopulation among mestizos that we named hspEuropePeru. This subpopulation seems to have more virulence-related elements than hspAmerind. Purifying selection driven by variable host immune response may have shaped the evolution of Peruvian subpopulations, potentially impacting disease outcomes.

19.
In Silico Biol ; 9(4): 149-62, 2009.
Artículo en Inglés | MEDLINE | ID: mdl-20109146

RESUMEN

Sporulation involves inducing scores of genes in a temporally and spatially coordinated cell development programme. Its initiation is controlled by an expanded two-component signal transduction system, termed a phosphorelay. The Spo0A response regulator is the master control element in the decision to sporulate, consisting of a receiver or phosphoacceptor domain and an effector or transcription activation domain having a high degree of sequence conservation. This study examined long-term Spo0A protein evolution for determining whether concerted evolution or purifying selection was the major factor in its evolution. The proportion of synonymous (pS) and non-synonymous nucleotide (pN) differences between Spo0A genes from 28 bacterial species was analysed. DIVERGE software was used for evaluating site-specific amino acids before phylogenetic divergence between Bacillus and Clostridium for detecting site-selective constrains operating on the Spo0A protein. Evolutionary Trace software was used for tracing the phylogenetic markers for this protein.


Asunto(s)
Proteínas Bacterianas/genética , Evolución Biológica , Esporas Bacterianas , Factores de Transcripción/genética , Secuencia de Aminoácidos , Bacillus/clasificación , Bacillus/genética , Bacillus/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Secuencia de Bases , Clostridium/clasificación , Clostridium/genética , Clostridium/metabolismo , Bases de Datos de Ácidos Nucleicos , Modelos Moleculares , Datos de Secuencia Molecular , Filogenia , Estructura Terciaria de Proteína , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Transducción de Señal/fisiología , Programas Informáticos , Esporas Bacterianas/genética , Esporas Bacterianas/metabolismo , Factores de Transcripción/química , Factores de Transcripción/metabolismo
20.
Food Sci Nutr ; 7(10): 3338-3348, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31660147

RESUMEN

Gari is a roasted fermented granular product made from cassava in many African countries. It is consumed raw, or added with water, or cooked into a paste. Up to now, gari enriched with palm oil and/or soybean is not available on Beninese markets. To our knowledge, no sensory profiling using appropriate methodology has been conducted on gari in Benin. The sensory studies on gari in Benin and other African countries only included general descriptors (appearance, taste, odor). The aim of our study was to establish a detailed sensory and physicochemical profile of nine traditional and three enriched gari made using different processes in Benin. Fifteen sensory descriptors of raw gari, and gari added with water, were generated and scored using quantitative descriptive analysis. The enriched gari differed from traditional gari mainly in color and odor, while their swelling capacity, texture during chewing, and light sour taste were similar. Marked variability in particle size, particle heterogeneity, water absorption, and sour taste was found among traditional gari. The physicochemical characteristics, such as degree of starch gelatinization, L-lactic acid, and ß-carotene contents, were highly variable among the 12 gari. Multifactor analysis revealed highly significant correlations between some physicochemical and sensory properties. The addition of soybean and/or palm oil did not affect most of the sensory properties of the traditional gari. The acceptability of these enriched gari with higher nutritive value by Beninese consumers should be tested to develop marketing strategies.

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