Apoplastomes of contrasting cacao genotypes to witches' broom disease reveals differential accumulation of PR proteins.

Witches' broom disease (WBD) affects cocoa trees (Theobroma cacao L.) and is caused by the fungus Moniliophthora perniciosa that grows in the apoplast in its biotrophic phase and later progresses into the tissues, causing serious losses in the production of cocoa beans. Therefore, the apoplast of T. cacao can provide important defense responses during the interaction with M. perniciosa. In this work, the protein profile of the apoplast of the T. cacao genotypes Catongo, susceptible to WBD, and CCN-51, resistant one, was evaluated. The leaves of T. cacao were collected from asymptomatic plants grown in a greenhouse (GH) and from green witches' brooms grown under field (FD) conditions for extraction of apoplastic washing fluid (AWF). AWF was used in proteomic and enzymatic analysis. A total of 14 proteins were identified in Catongo GH and six in Catongo FD, with two proteins being common, one up-accumulated, and one down-accumulated. In CCN-51, 19 proteins were identified in the GH condition and 13 in FD, with seven proteins being common, one up-accumulated, and six down-accumulated. Most proteins are related to defense and stress in both genotypes, with emphasis on pathogenesis-related proteins (PR): PR-2 (ß-1,3-glucanases), PR-3 and PR-4 (chitinases), PR-5 (thaumatine), PR-9 (peroxidases), and PR-14 (lipid transfer proteins). Furthermore, proteins from microorganisms were detected in the AWF. The enzymatic activities of PR-3 showed a significant increase (p < 0.05) in Catongo GH and PR-2 activity (p < 0.01) in CCN-51 FD. The protein profile of the T. cacao apoplastome offers insight into the defense dynamics that occur in the interaction with the fungus M. perniciosa and offers new insights in exploring future WBD control strategies.

A repertoire of candidate effector proteins of the fungus Ceratocystis cacaofunesta.

The genus Ceratocystis includes many phytopathogenic fungi that affect different plant species. One of these is Ceratocystis cacaofunesta, which is pathogenic to the cocoa tree and causes Ceratocystis wilt, a lethal disease for the crop. However, little is known about how this pathogen interacts with its host. The knowledge and identification of possible genes encoding effector proteins are essential to understanding this pathosystem. The present work aimed to predict genes that code effector proteins of C. cacaofunesta from a comparative analysis of the genomes of five Ceratocystis species available in databases. We performed a new genome annotation through an in-silico analysis. We analyzed the secretome and effectorome of C. cacaofunesta using the characteristics of the peptides, such as the presence of signal peptide for secretion, absence of transmembrane domain, and richness of cysteine residues. We identified 160 candidate effector proteins in the C. cacaofunesta proteome that could be classified as cytoplasmic (102) or apoplastic (58). Of the total number of candidate effector proteins, 146 were expressed, presenting an average of 206.56 transcripts per million. Our database was created using a robust bioinformatics strategy, followed by manual curation, generating information on pathogenicity-related genes involved in plant interactions, including CAZymes, hydrolases, lyases, and oxidoreductases. Comparing proteins already characterized as effectors in Sordariomycetes species revealed five groups of protein sequences homologous to C. cacaofunesta. These data provide a valuable resource for studying the infection mechanisms of these pathogens in their hosts.

A Historical Twist on Long-Range Wireless: Building a 103 km Multi-Hop Network Replicating Claude Chappe's Telegraph.

In 1794, French Engineer Claude Chappe coordinated the deployment of a network of dozens of optical semaphores. These formed "strings" that were hundreds of kilometers long, allowing for nationwide telegraphy. The Chappe telegraph inspired future developments of long-range telecommunications using electrical telegraphs and, later, digital telecommunication. Long-range wireless networks are used today for the Internet of Things (IoT), including industrial, agricultural, and urban applications. The long-range radio technology used today offers approximately 10 km of range. Long-range IoT solutions use "star" topology: all devices need to be within range of a gateway device. This limits the area covered by one such network to roughly a disk of a 10 km radius. In this article, we demonstrate a 103 km low-power wireless multi-hop network by combining long-range IoT radio technology with Claude Chappe's vision. We placed 11 battery-powered devices at the former locations of the Chappe telegraph towers, hanging under helium balloons. We ran a proprietary protocol stack on these devices so they formed a 10-hop multi-hop network: devices forwarded the frames from the "previous" device in the chain. This is, to our knowledge, the longest low power multi-hop wireless network built to date, demonstrating the potential of combining long-range radio technology with multi-hop technology.

Structural Analysis of the Spike Protein of SARS-CoV-2 Variants and Other Betacoronaviruses Using Molecular Dynamics.

A structural analysis over various spike proteins from three highly pathogenic Betacoronavirus was done to understand their structural differences. The proteins were modeled using crystal structures from SARS-CoV, MERS-CoV, and other Betacoronavirus that infect bats and pangolins. The group was split in two sets; the first set corresponds to the non-mutated spike proteins, while the second set corresponds to mutated spike variants alpha, beta, gamma, delta, omicron and mu; five of them classified as variants of concern and the last one as variant of interest. A conformational space exploration was carried out for every protein by using molecular dynamic simulations. Root mean square fluctuations, principal component and cross-correlation analysis were carried out over the dynamics to analyze the flexibility and rigidity of every protein in comparison to the wild type Spike protein from the SARS-CoV-2. The obtained results indicate that the proteins, which are not spread among humans, have smooth movements compared to those of SARS-CoV-2 and its variants. In addition, a relationship between the speed of the virulence and the movement of the protein can explain the behavior of delta and omicron variants.

Optimization of fractional-order chaotic cellular neural networks by metaheuristics.

Artificial neural networks have demonstrated to be very useful in solving problems in artificial intelligence. However, in most cases, ANNs are considered integer-order models, limiting the possible applications in recent engineering problems. In addition, when dealing with fractional-order neural networks, almost any work shows cases when varying the fractional order. In this manner, we introduce the optimization of a fractional-order neural network by applying metaheuristics, namely: differential evolution (DE) and accelerated particle swarm optimization (APSO) algorithms. The case study is a chaotic cellular neural network (CNN), for which the main goal is generating fractional orders of the neurons whose Kaplan-Yorke dimension is being maximized. We propose a method based on Fourier transform to evaluate if the generated time series is chaotic or not. The solutions that do not have chaotic behavior are not passed to the time series analysis (TISEAN) software, thus saving execution time. We show the best solutions provided by DE and APSO of the attractors of the fractional-order chaotic CNNs.

Structural and Functional Genomics of the Resistance of Cacao to Phytophthora palmivora.

Black pod disease, caused by Phytophthora spp., is one of the main diseases that attack cocoa plantations. This study validated, by association mapping, 29 SSR molecular markers flanking to QTL (Quantitative Trait Loci) associated with Phytophthora palmivora Butler (Butler) (PP) resistance, in three local ancient varieties of the Bahia (Comum, Pará, and Maranhão), varieties that have a high potential in the production of gourmet chocolate. Four SSR loci associated with resistance to PP were detected, two on chromosome 8, explaining 7.43% and 3.72% of the Phenotypic Variation (%PV), one on chromosome 2 explaining 2.71%PV and one on chromosome 3 explaining 1.93%PV. A functional domains-based annotation was carried out, in two Theobroma cacao (CRIOLLO and MATINA) reference genomes, of 20 QTL regions associated with cocoa resistance to the pathogen. It was identified 164 (genome CRIOLLO) and 160 (genome MATINA) candidate genes, hypothetically involved in the recognition and activation of responses in the interaction with the pathogen. Genomic regions rich in genes with Coiled-coils (CC), nucleotide binding sites (NBS) and Leucine-rich repeat (LRR) domains were identified on chromosomes 1, 3, 6, 8, and 10, likewise, regions rich in Receptor-like Kinase domain (RLK) and Ginkbilobin2 (GNK2) domains were identified in chromosomes 4 and 6.

Chaotic Image Encryption Using Hopfield and Hindmarsh-Rose Neurons Implemented on FPGA.

Chaotic systems implemented by artificial neural networks are good candidates for data encryption. In this manner, this paper introduces the cryptographic application of the Hopfield and the Hindmarsh-Rose neurons. The contribution is focused on finding suitable coefficient values of the neurons to generate robust random binary sequences that can be used in image encryption. This task is performed by evaluating the bifurcation diagrams from which one chooses appropriate coefficient values of the mathematical models that produce high positive Lyapunov exponent and Kaplan-Yorke dimension values, which are computed using TISEAN. The randomness of both the Hopfield and the Hindmarsh-Rose neurons is evaluated from chaotic time series data by performing National Institute of Standard and Technology (NIST) tests. The implementation of both neurons is done using field-programmable gate arrays whose architectures are used to develop an encryption system for RGB images. The success of the encryption system is confirmed by performing correlation, histogram, variance, entropy, and Number of Pixel Change Rate (NPCR) tests.

An evaluation of monovalent, divalent, and trivalent cations as aggregating agents for surface enhanced Raman spectroscopy (SERS) analysis of synthetic cannabinoids.

In this study monovalent, divalent, and trivalent chloride, sulfate and nitrate salts were examined to determine the critical coagulation concentration (CCC) for each salt and its corresponding effect on detection limits for SERS analysis of cannabinoid extracts. The CCC of each salt was determined using UV-vis, particle size and zeta potential measurements. The results demonstrated that the divalent and trivalent cations produce a lower CCC when compared to monovalent cations. The data indicate the effect that cation valence has on nanoparticle destabilization. This information is essential because it permits the user to develop optimal conditions for aggregation of salts used in SERS. Tests were then performed to determine the best conditions for SERS detection of a small set of cannabinoids with naphthyl indole moieties. The results demonstrate the importance of salt concentration for colloid aggregation and illustrate the effect of aggregation on sensitivity for the SERS experiment.

Evaluation of IEEE802.15.4g for Environmental Observations.

IEEE802.15.4g is a low-power wireless standard initially designed for Smart Utility Networks, i.e., for connecting smart meters. IEEE802.15.4g operates at sub-GHz frequencies to offer 2⁻3× longer communication range compared to its 2.4 GHz counterpart. Although the standard offers 3 PHYs (Frequncy Shift Keying, Orthogonal Frequency Division Multiplexing and Offset-Quadrature Phase Shift Keying) with numerous configurations, 2-FSK at 50 kbps is the mandatory and most prevalent radio setting used. This article looks at whether IEEE802.15.4g can be used to provide connectivity for outdoor deployments. We conduct range measurements using the totality of the standard (all modulations with all further parametrization) in the 863⁻870 MHz band, within four scenarios which we believe cover most low-power wireless outdoor applications: line of sight, smart agriculture, urban canyon, and smart metering. We show that there are radio settings that outperform the "2-FSK at 50 kbps" base setting in terms of range, throughput and reliability. Results show that highly reliable communications with data rates up to 800 kbps can be achieved in urban environments at 540 m between nodes, and the longest useful radio link is obtained at 779 m. We discuss how IEEE802.15.4g can be used for outdoor operation, and reduce the number of repeater nodes that need to be placed compared to a 2.4 GHz solution.

Proof of Concept: Development of Snow Liquid Water Content Profiler Using CS650 Reflectometers at Caribou, ME, USA.

The quantity of liquid water in the snowpack defines its wetness. The temporal evolution of snow wetness's plays a significant role in wet-snow avalanche prediction, meltwater release, and water availability estimations and assessments within a river basin. However, it remains a difficult task and a demanding issue to measure the snowpack's liquid water content (LWC) and its temporal evolution with conventional in situ techniques. We propose an approach based on the use of time-domain reflectometry (TDR) and CS650 soil water content reflectometers to measure the snowpack's LWC and temperature profiles. For this purpose, we created an easily-applicable, low-cost, automated, and continuous LWC profiling instrument using reflectometers at the Cooperative Remote Sensing Science and Technology Center-Snow Analysis and Field Experiment (CREST-SAFE) in Caribou, ME, USA, and tested it during the snow melt period (February-April) immediately after installation in 2014. Snow Thermal Model (SNTHERM) LWC simulations forced with CREST-SAFE meteorological data were used to evaluate the accuracy of the instrument. Results showed overall good agreement, but clearly indicated inaccuracy under wet snow conditions. For this reason, we present two (for dry and wet snow) statistical relationships between snow LWC and dielectric permittivity similar to Topp's equation for the LWC of mineral soils. These equations were validated using CREST-SAFE in situ data from winter 2015. Results displayed high agreement when compared to LWC estimates obtained using empirical formulas developed in previous studies, and minor improvement over wet snow LWC estimates. Additionally, the equations seemed to be able to capture the snowpack state (i.e., onset of melt, medium, and maximum saturation). Lastly, field test results show advantages, such as: automated, continuous measurements, the temperature profiling of the snowpack, and the possible categorization of its state. However, future work should focus on improving the instrument's capability to measure the snowpack's LWC profile by properly calibrating it with in situ LWC measurements. Acceptable validation agreement indicates that the developed snow LWC, temperature, and wetness profiler offers a promising new tool for snow hydrology research.

Xpert MTB/RIF(r) como herramienta diagnóstica en una cohorte de niños menores de 15 años con sospecha clínica de tuberculosis pulmonar en un hospital de alta complejidad de Medellín / Xpert MTB/RIF(r) as a diagnostic tool in a cohort of children under 15 years of age with clinical suspicion of pulmonary tuberculosis in a hospital of high complexity in Medellin

Introducción: La tuberculosis (TB) en niños posee limitaciones en la confirmación microbiológica. Por su naturaleza paucibacilar y la dificultad para obtener muestras microbiológicas adecuadas, la positividad de cultivos es baja. En adultos, la prueba Gene Xpert MTB/RIF(r) ha mostrado utilidad por su buen rendimiento, rapidez de resultados y facilidad en su realización. La Organización Mundial de la Salud (OMS) recomienda el empleo de esta prueba en niños, sin embargo, los datos de esta prueba en nuestro medio son limitados. Objetivo: Estudio de cohorte retrospectivo para describir nuestra experiencia con la prueba Gene Xpert MTB/RIF en menores de 15 años hospitalizados en un centro de alta complejidad con sospecha de TB pulmonar. Método: Se revisaron 116 historias clínicas con resultados disponibles de Xpert MTB/RIF en muestras respiratorias tomadas entre junio de 2012 y diciembre de 2013. Se excluyeron 33 casos. Los 83 pacientes incluidos se clasificaron como: TB confirmada 8 (10%), probable 16 (19%) y descartada 59 (71%) según criterios de la OMS. El análisis estadístico se realizó en SPSS 20 y EpiDat 3.1. Resultados: Xpert MTB/RIF mostró para TB confirmada una sensibilidad del 50%, especificidad 96% y valores predictivos positivos y negativos del 57,14 y 94,7%, respectivamente. Al evaluarla en el total de niños que ameritaron inicio de tratamiento (TB confirmada y probable), la sensibilidad fue del 29% con especificidad del 100%. Xpert MTB/RIF detectó una cepa resistente a rifampicina. Conclusión: Xpert MTB/RIF mostró ser útil para el diagnóstico de TB, con una sensibilidad superior a la baciloscopia. Un resultado positivo puede definir el inicio temprano de tratamiento en casos dudosos, confirma el diagnóstico y permite conocer rápidamente si existe resistencia a rifampicina. Un resultado negativo no descarta el diagnóstico ni debe impedir el inicio del tratamiento si cumple con la sumatoria de los otros criterios recomendados por la OMS.

Introduction: Microbiological confirmation of tuberculosis (TB) in children is difficult. Due to its paucibacillary course, the positivity of cultures is low and samples are not easy to obtain. In adults, Genexpert MTB/RIF is useful for diagnosing TB. It shows good test performance, offers fast results and is a simple technique for laboratory personnel. The World Health Organization (WHO) recommends its use for children, but clinical studies on this age group are scarce. Objective: This was a retrospective, descriptive cohort study. The purpose of this study was to describe our experience with Gene Xpert MTB/RIF in children younger than 15 years of age with clinical suspicion of pulmonary TB, who were admitted to a high complexity hospital. Methods: A total of 116 clinical charts with available results of Xpert MTB/RIF in respiratory samples taken between June 2012 and December 2013 were reviewed and of these, 33 were excluded. The 83 included patients were classified according to the WHO criteria into confirmed TB (n = 8; 10%), probable (n = 16; 19%) and no TB (n = 59; 71%). An analysis was performed using SPSS 20 and EpiDat 3.1. Results: The Xpert MTB/RIF was 50% sensitive and 96% specific, with a positive predictive value of 57.14% and an negative predictive value of 94.7% for children with confirmed TB. When evaluating Xpert MTB/RIF in all children who received TB treatment (confirmed plus probable TB disease) the sensitivity was 29% with 100% specificity. Among our cohort, the Xpert MTB/RIF detected one child with rifampicin resistance. Conclusions: Xpert MTB/RIF was useful for the diagnosis of TB. A positive result can lead to the early initiation of treatment in doubtful cases. It confirms the diagnosis and quickly reveals rifampicin resistance. A negative result, however, just as with cultures, does not exclude the diagnosis and should not prevent the initiation of treatment, if it is considered needed based on other criteria.

Toxoplasma gondii and Giardia duodenalis infections in domestic dogs in New York City public parks.

Toxoplasma gondii and Giardia duodenalis have been widely reported to produce major diseases in humans and domestic animals. Little is known about the occurrence of these protozoan parasites in domestic dogs in the United States. The goal of this study was to determine the prevalence and genotypes of T. gondii and G. duodenalis among dogs in New York City. Fecal samples from domestic dogs were analyzed by polymerase chain reaction (PCR). Overall, 3% of the samples tested positive for T. gondii, while 15% were positive for G. duodenalis. PCR-RFLP of T. gondii-positive samples revealed genotypes I and III, while sequence analysis of the G. duodenalis-positive samples indicated that 94.1% of the dogs were infected with the zoonotic assemblage A. Further studies are needed to determine the prevalence of zoonotic protozoan parasites in domestic dogs.

Características clínicas de los pacientes menores de 18 años con atrofia muscular espinal en Medellín, 2008 - 2013 / Clinical characteristics of patients under 18 years-old with spinal muscular atrophy in Medellín, 2008 - 2013

Introducción: La atrofia muscular espinal (AME) es una enfermedad degenerativa que afecta las neuronas motoras del asta anterior de la médula espinal, se manifiesta por debilidad muscular progresiva de predominio proximal, hipotonía y arreflexia osteotendinosa, la etiología es una mutación en el gen de supervivencia neuronal SMN. Objetivo: determinar las características clínicas de los pacientes menores de 18 años con atrofia muscular espinal en de Medellín, durante el período 2008-2013. Materiales y métodos: se realizó un estudio descriptivo retrospectivo de los pacientes con AME que consultaron en el Hospital Universitario San Vicente Fundación y un consultorio privado de neuropediatría en Medellín durante el período 2008-2013, en total se recopilaron datos de 29 pacientes, se revisaron las características clínicas, las ayudas diagnósticas practicadas y los tratamientos realizados. Resultados: la AME tipo II resultó la forma clínica más frecuente (62%) seguida por la AME tipo I (24.13%), las principales manifestaciones fueron la hipotonía (100%) debilidad muscular (93.1%) y la arreflexia osteotendinosa (82.8%). Las fasciculaciones en la lengua se presentaron en el 48.3% de los pacientes. La prueba molecular fue realizada en 6 pacientes y en todos se encontró deleción del exón 7 del gen SMN1. Conclusión: la atrofia muscular espinal es una enfermedad degenerativa y de progresión variable de acuerdo a su clasificación. Clínicamente, se debe sospechar cuando exista síndrome motoneuronal y fasciculaciones linguales. El diagnóstico molecular es el método más acertado para confirmar la enfermedad.

Introduction: Spinal muscular atrophy (SMA) is a degenerative disease that affects motor neurons in the anterior horn of the spinal cord, it is manifested by progressive muscle weakness predominantly proximal, hypotonia andosteotendinous arreflexia, the cause is a mutation in neuronal survival gene SMN1 Objective: Establish the clinical, electromyographics and genetics characteristics of patients younger than 18 years with spinal muscular atrophy in the Medellín city, during the period 2008-2013. Materials and methods: A retrospective study of patients with SMA seen in the Hospital Universitario San Vicente Foundation and private center of Neuro- pediatric of Medellín during the period 2008-2013 was performed. Data from 29 patientes were available, were reviewed clinical feature, diagnostic aids and treatments practiced. Results: SMA type II resulted the most frequent clinical presentation (62%) followed by SMA type I (24.13%), the main manifestations were hypotonia (100 %), muscle weakness (93.1%) and osteotendinous arreflexia (82.8%), tongue fasciculations occurred in 48.3% of patients. The molecular test was performed in 6 patients and in all the deletion of exon 7 of the SMN1 gene was found. Conclusion: spinal muscular atrophy is a degenerative and progressive disease according to their clinical classification. It should be suspected when there are motoneuronal syndrome and lingual twitches. Molecular diagnosis is the most accurate to confirm the disease.

Bioavailability of heme iron in biscuit filling using piglets as an animal model for humans.

The objective of this work was to evaluate the bioavailability of heme iron added to biscuit filling. It comprised two stages: first, the development of the heme iron enriched biscuit filling; second, the evaluation of the bioavailability of the mineral in fattening piglets. Two groups were selected randomly and fed: a) Low iron feed and biscuits with heme iron supplemented filling; b) Normal feed (with ferrous sulphate). Weight and blood parameters were measured every fifteen days. Averages were compared after duplicate analyses. The filling had a creamy appearance, chocolate taste and smell, appropriate spreadability, heme iron content of 2.6 mg per gram and a shelf-life of a month. The heme iron supplemented pigs registered a greater (P<0.05) weight gain (27.8% more than the control group). Mortality in the heme iron group was 10%, compared to 50% in the control group. The amount of iron measured in the different compartment was greater in the heme group (3315 mg) than in the control group (2792 mg). However, the amount of iron consumed in the latter was greater. We show that an acceptable product with high heme iron content can be formulated, suitable for use as biscuit filling. The heme iron supplement produced better weight increase and lesser mortality in fattening pigs. The bioavailability of heme iron was 23% greater (P<0.05) compared to ferrous sulphate.