Biology subjects

Luis, A.

Publications and source records attributed to Luis, A..

6 recordsLinked to original sources

bioRxiv2026

snputils: A High-Performance Python Library for Genetic Variation and Population Structure

The increasing size and resolution of genomic and population genetic datasets offer unprecedented opportunities to study population structure and uncover the genetic basis of complex traits and diseases. The collection of existing analytical tools, however, is characterized by format incompatibilities, limited functionality, and computational inefficiencies, forcing researchers to construct fragile pipelines that chain together fragmented command-line utilities and ad hoc scripts. These are difficult to maintain, scale, and reproduce. To address such limitations, we present snputils, a Python library that unifies high-performance I/O, transformation, and analysis of genotype, ancestry, and phenotypic information within a single framework suitable for biobank-scale research. The library provides efficient tools for essential operations, including querying, cleaning, merging, and statistical analysis. In addition, it offers classical population genetic statistics with optional ancestry-specific masking. An identity-by-descent module supports reading of multiple formats, filtering and ancestry-restricted segment trimming for relatedness and demographic inference. snputils also incorporates ancestry-masking and multi-array functionalities for dimensionality reduction methods, as well as efficient implementations of admixture simulation, admixture mapping, and advanced visualization capabilities. With support for the most commonly used file formats, snputils integrates smoothly with existing tools and clinical databases. At the same time, its modular and optimized design reduces technical overhead, facilitating reproducible workflows that accelerate discoveries in population genetics, genomic research, and precision medicine. Benchmarking demonstrates a significant reduction in genotype data loading speed compared to existing Python libraries. The open-source library is available at https://github.com/AI-sandbox/snputils, with full documentation and tutorials at snputils.org.

bioinformatics↗

bioRxiv2023

Reference materials for SARS-CoV-2 molecular diagnostic: validation of encapsulated synthetic RNAs for room temperature storage and shipping

The Coronavirus pandemic unveiled the unprecedented need for diagnostic tests to rapidly detect the presence of pathogens in the population. Real-time RT-PCR and other nucleic acid amplification techniques are accurate and sensitive molecular techniques that necessitate positive controls. To meet this need, Twist Bioscience has developed and released synthetic RNA controls. However, RNA is an inherently unstable molecule needing cold storage, costly shipping, and resource-intensive logistics. Imagene provides a solution to this problem by encapsulating dehydrated RNA inside metallic capsules filled with anhydrous argon, allowing room temperature and eco-friendly storage and shipping. Here, RNA controls produced by Twist were encapsulated (RNAshells) and distributed to several laboratories that used them for COVID-19 detection tests by amplification. One RT-LAMP procedure, four different RT-PCR devices and 6 different PCR kits were used. The amplification targets were genes E, N; RdRp, Sarbeco-E and Orf1a/b. RNA retrieval was satisfactory, and the detection was reproducible. RNA stability was checked by accelerated aging. The results for a 10-year equivalent storage time at 25 {degrees}C were not significantly different from those for unaged samples. This room temperature RNA stability allows the preparation and distribution of large strategic batches which can be stored for a long time and used for standardization processes between detection sites. Moreover, it makes it also possible to use these controls for single use and in the field where large temperature differences can occur. Consequently, this type of encapsulated RNA controls, processed at room temperature, can be used as reference materials for the SARS-Cov-2 virus as well as for other pathogens detection.

molecular biology↗

bioRxiv2021

Long term conservation of DNA at ambient temperature. Implications for DNA data storage

DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25 {degrees}C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

biochemistry↗

bioRxiv2020

Circadian rhythms in bipolar disorder patient-derived neurons predict lithium response

Bipolar disorder (BD) is a neuropsychiatric disorder with genetic risk factors defined by recurrent episodes of mania/hypomania, depression and circadian rhythm abnormalities. While lithium is an effective drug for BD, 30-40% of patients fail to respond adequately to treatment. Previous work has demonstrated that lithium affects the expression of "clock genes" and that lithium responders (Li-R) can be distinguished from non-responders (Li-NR) by differences in circadian rhythms. However, rhythm abnormalities in BD have not been evaluated in neurons and it is unknown if neuronal rhythms differ between Li-R and Li-NR. We used induced pluripotent stem cells (iPSCs) to culture neuronal precursor cells (NPC) and glutamatergic neurons from BD patients and controls. We identified strong circadian rhythms in Per2-luc expression in NPCs and neurons from controls and Li-R. NPC rhythms in Li-R had a shorter circadian period. Li-NR rhythms were low-amplitude and profoundly weakened. In NPCs and neurons, expression of PER2 was higher in both BD groups compared to controls. In neurons, PER2 protein expression was higher in BD than controls, especially in Li-NR samples. In single cells, NPC and neuron rhythms in both BD groups were desynchronized compared to controls. Lithium lengthened period in Li-R and control neurons but failed to alter rhythms in Li-NR. In contrast, temperature entrainment increased amplitude across all groups, and partly restored rhythms in Li-NR neurons. We conclude that neuronal circadian rhythm abnormalities are present in BD and most pronounced in Li-NR. Rhythm deficits in BD may be partly reversible through stimulation of entrainment pathways.

neuroscience↗

bioRxiv2019

A genetically adaptable strategy for ribose scavenging in a human gut symbiont plays a diet-dependent role in colon colonization

Efficient nutrient acquisition in the competitive human gut is essential for microbial persistence. While polysaccharides have been well-studied nutrients for the gut microbiome, other resources such as co-factors and nucleic acids have been less examined. We describe a series of ribose utilization systems (RUSs) that are broadly represented in Bacteroidetes and appear to have diversified to allow access to ribose from a variety of substrates. One Bacteroides thetaiotaomicron RUS variant is critical for competitive gut colonization in a diet-specific fashion. Using molecular genetics, we probed the nature of the ribose source underlying this diet-specific phenotype, revealing that hydrolytic functions in RUS (e.g., to cleave ribonucleosides) are present but dispensable. Instead, ribokinases that are activated in vivo and participate in cellular ribose-phosphate metabolism are essential. Our results underscore the extensive mechanisms that gut symbionts have evolved to access nutrients and how metabolic context determines the impact of these functions in vivo.

microbiology↗

bioRxiv2018

Pinnularia baetica sp. nov. (Bacillarophyceae): a new diatom species found in an alkaline mountain lagoon in the south of Europe (Granada, Spain)

A new benthic freshwater diatom species belonging to the genus Pinnularia was found in Laguna Seca of Sierra Seca in the north of the province of Granada, Spain. Pinnularia baetica sp.nov. is proposed as a new species based on observations under light (LM) and scanning electron microscopy (SEM) and its special ecology typical of a calcareous lagoon. The most similar taxa to P. baetica is P. atlasii and with more differences P. infirma and the last two were studied through material obtained in lagoons of northern Morocco. Although there are similarities in the morphological characters of the frustule, it was possible to verify through LM and SEM micrographs, evident differences between P. baetica and the other two taxa; on the one end, P. baetica has a panduriform shape more pronounced than P. infirma and bigger size. On the other hand, the absence of spines in P. baetica and the more convergent striation at the poles are the main differences with P. atlasi.\n\nPhylum Ochrophyta Caval.-Sm. (Cavalier-Smith 1995)\n\nClass Bacillariophyceae Haeckel emend. Medlin & Kaczmarska (Medlin & Kaczmarska 2004)\n\nSubclass Bacillariophycidae Round (Round et al. 1990)\n\nOrder Naviculales (Bessey 1907 sensu emend)\n\nFamily Pinnulariaceae D.G. Mann, 1990, Genus Pinnularia C.G. Ehrenberg, 1843\n\nPinnularia baetica Fernandez Moreno & Sanchez Castillo sp. nov

plant biology↗