'Gel-Stacks' gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study.

Large DNA molecules (>20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be 'rescued' as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed 'Gel-Stacks.' Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion.

A database of restriction maps to expand the utility of bacterial artificial chromosomes.

While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read technologies. Such libraries may now serve as a valuable resource for manipulating and assembling large genomic constructs. To enhance accessibility and comparison, we have developed a BAC restriction map database. Using information from the National Center for Biotechnology Information's cloneDB FTP site, we constructed a database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of the available restriction enzymes. Along with the database, we generated a set of Python functions to reconstruct the database and more easily access the information within. This data is valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.

Oropouche virus as an emerging cause of acute febrile illness in Colombia.

Arbovirus infections are frequent causes of acute febrile illness (AFI) in tropical countries. We conducted health facility-based AFI surveillance at four sites in Colombia (Cucuta, Cali, Villavicencio, Leticia) during 2019-2022. Demographic, clinical and risk factor data were collected from persons with AFI that consented to participate in the study (n = 2,967). Serologic specimens were obtained and tested for multiple pathogens by RT-PCR and rapid test (Antigen/IgM), with 20.7% identified as dengue positive from combined testing. Oropouche virus (OROV) was initially detected in serum by metagenomic next-generation sequencing (mNGS) and virus target capture in a patient from Cúcuta. Three additional infections from Leticia were confirmed by conventional PCR, sequenced, and isolated in tissue culture. Phylogenetic analysis determined there have been at least two independent OROV introductions into Colombia. To assess OROV spread, a RT-qPCR dual-target assay was developed which identified 87/791 (10.9%) viremic cases in AFI specimens from Cali (3/53), Cucuta (3/19), Villavicencio (38/566), and Leticia (43/153). In parallel, an automated anti-nucleocapsid antibody assay detected IgM in 27/503 (5.4%) and IgG in 92/568 (16.2%) patients screened, for which 24/68 (35.3%) of PCR positives had antibodies. Dengue was found primarily in people aged <18 years and linked to several clinical manifestations (weakness, skin rash and petechiae), whereas Oropouche cases were associated with the location, climate phase, and odynophagia symptom. Our results confirm OROV as an emerging pathogen and recommend increased surveillance to determine its burden as a cause of AFI in Colombia.

Use of oral fluids for efficient monitoring of influenza viruses in swine herds in Colombia

Background: Influenza A virus (IAV) surveillance in swine is critical not only due to the direct impact of the disease in the pork industry but also because IAV are prone to interspecies transmission (from human to pigs and vice versa); therefore, its monitoring is fundamental from a public and animal health perspective. Several diagnostic techniques have been used to detect IAV infection from nasal samples in swine, while samples of oral fluids (OF) are in use as novel alternatives for pathogen detection. The OF allow for efficient and feasible low-cost disease detection at the herd level, with low risk of stress for the animals. Objective: To describe a surveillance strategy of IAV at the herd level during respiratory disease outbreaks in swine farms at tropical settings using porcine oral fluids. Methods: An active surveillance strategy was conducted in several farms with past records of respiratory disease. The IAV detection was conducted in five purposively selected swine farms from years 2014 to 2017. We investigated a total of 18 respiratory outbreaks of the disease. Swine OF were collected for IAV testing. An OF sample is described as a pen-based specimen collected from a group of >20 pigs per pen and/or per barn (stall-housed individually with close contact among them). The IAV infection was investigated in OF by rRT-PCR testing and confirmed by viral isolation in cell culture Results: We found 107 (7.4%) positives to IAV by rRT-PCR from a total of 1,444 OF samples tested. Additionally, 9 IAV isolates were all further identified as H1 subtype. Conclusions: Our results demonstrate that OF can be easily implemented as a novel, user-friendly, welfare-friendly, accurate and cost-effective sampling method for active surveillance and monitoring of IAV infections in swine farms in tropical settings.

Antecedentes: La vigilancia del Virus Influenza A (IAV) en los cerdos es fundamental debido al impacto directo de la enfermedad en la industria porcina, pero también porque los IAV son propensos de transmisión entre especies (humanos a cerdos y viceversa), y por lo tanto su monitoreo es crítico desde las perspectivas de salud pública y animal. Actualmente existen varias técnicas de diagnóstico disponibles para detectar la infección por IAV a partir de muestras nasales en cerdos, sin embargo, se han implementado otras muestras como los fluidos orales (OF) como nuevas alternativas para la detección de patógenos. El OF permite una detección eficiente y factible de enfermedades a menor costo a nivel de rebaño, con menor riesgo de estrés para los animales. Objetivo: Describir una estrategia de vigilancia de IAV a nivel de hato por medio de fluidos orales porcinos durante brotes de enfermedades respiratorias en granjas porcinas en entornos tropicales. Métodos: Se llevó a cabo una estrategia de vigilancia activa en cinco granjas porcinas seleccionadas con antecedentes de enfermedades respiratorias. Se recolectaron OF porcinos para la prueba de IAV. Una muestra de OF se describió como una muestra grupal recolectada de un grupo de >20 cerdos por corral y/o por establo (si estaban alojados individualmente, pero tenían un contacto cercano entre ellos). La infección por IAV se investigó probando OF mediante rRT-PCR y la confirmación mediante aislamiento viral en cultivo celular. Resultados: La detección de IAV se llevó a cabo en cinco granjas seleccionadas intencionalmente entre 2014- 2017. Investigamos un total de 18 eventos de brotes de enfermedades respiratorias. Del total de 1.444 OF muestras analizadas, encontramos 107 (7,4%) positivos a IAV mediante rRT-PCR. Además, solo se obtuvieron 9 aislamientos de IAV y todos se identificaron además como subtipo H1. Conclusiones: Los resultados de nuestro estudio demostraron cómo la OF puede implementarse fácilmente como un método de muestreo novedoso, fácil de usar, amigable con el bienestar animal, preciso y rentable para la vigilancia activa y el monitoreo de infecciones por IAV en granjas porcinas en entornos tropicales.

Antecedentes: A vigilância do vírus Influenza A (IAV) em suínos é crítica devido ao impacto direto da doença na indústria de suínos, mas também porque os IAV são propensos a transmissão interespécies (de humanos para porcos e vice-versa) e, portanto, seu monitoramento é crítico do ponto de vista da saúde pública e animal. Atualmente, existem várias técnicas de diagnóstico disponíveis para detectar a infecção por IAV em amostras nasais de suínos, no entanto, outras amostras, como fluidos orais (OF), têm sido implementadas como novas alternativas para a detecção de patógenos. O OF permite uma detecção eficiente e viável de doenças com menor custo em nível de rebanho, com menor risco de estresse para os animais. Objetivo: Descrever uma estratégia de vigilância de IAV em nível de rebanho durante surtos de doenças respiratórias em granjas de suínos em ambientes tropicais por meio de fluidos orais suínos. Métodos: A estratégia de vigilância ativa foi conduzida em cinco granjas de suínos selecionadas com histórico de doenças respiratórias. Suínos OF foram coletados para teste de IAV. Uma amostra OF foi descrita como um espécime baseado em curral coletado de um grupo de >20 porcos por curral e/ou por celeiro (se eles foram alojados individualmente, mas tendo contato próximo entre eles). A infecção IAV foi investigada testando OF por rRT-PCR e confirmada por isolamento em cultura de células. Resultados: A detecção do IAV foi realizada em cinco fazendas selecionadas propositalmente entre 2014-2017. Nós investigamos um total de 18 eventos de surto de doença respiratória. Do total de 1.444 amostras de OF testadas, encontramos 107 (7,4%) positivas para IAV por rRT-PCR. Além disso, apenas 9 isolados de IAV foram obtidos, e todos foram posteriormente identificados como subtipo H1. Conclusão: Os resultados de nosso estudo demonstraram como o OF pode ser facilmente implementado como um método de amostragem novo, amigável, amigável com o bem-estar, preciso e de baixo custo para vigilância ativa e monitoramento de infecções IAV em fazendas de suínos em ambientes tropicais.

Prolate and oblate chiral liquid crystal spheroids.

Liquid crystals are known to exhibit intriguing textures and color patterns, with applications in display and optical technologies. This work focuses on chiral materials and examines the palette of morphologies that arises when microdroplets are deformed into nonspherical shapes in a controllable manner. Specifically, geometrical confinement and mechanical strain are used to manipulate orientational order, phase transitions, and topological defects that arise in chiral liquid crystal droplets. Inspired by processes encountered in nature, where insects and animals often rely on strain and temperature to alter the optical appearance of dispersed liquid crystalline elements, chiral droplets are dispersed in polymer films and deformation induced by uniaxial or biaxial stretching. Our measurements are interpreted by resorting to simulations of the corresponding systems, thereby providing an in-depth understanding of the morphologies that arise in these materials. The reported structures and assemblies offer potential for applications in smart coatings, smart fabrics, and wearable sensors.