Sparse Negative Binomial Signal Recovery for Genomic Variant Prediction in Diploid Species.

Structural variants (SVs) - such as insertions, deletions, and duplications of an individual's genome - are associated with genetic diseases and promotion of genetic diversity. Detecting SVs of an unknown genome is a mathematically challenging problem since SVs are rare and prone to low-coverage noise. Common approaches to detect SVs in an unknown genome require sequencing fragments of the genome, comparing them to a high-quality reference genome, and predicting SVs based on identified discordant fragments.

Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals.

Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution.

NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency.

The National Institute of Health (NIH) Library of integrated network-based cellular signatures (LINCS) program is premised on the generation of a publicly available data resource of cell-based biochemical responses or "signatures" to genetic or environmental perturbations. NeuroLINCS uses human inducible pluripotent stem cells (hiPSCs), derived from patients and healthy controls, and differentiated into motor neuron cell cultures. This multi-laboratory effort strives to establish i) robust multi-omic workflows for hiPSC and differentiated neuronal cultures, ii) public annotated data sets and iii) relevant and targetable biological pathways of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS).

Associations between forensic loci and expression levels of neighboring genes may compromise medical privacy.

A set of 20 short tandem repeats (STRs) is used by the US criminal justice system to identify suspects and to maintain a database of genetic profiles for individuals who have been previously convicted or arrested. Some of these STRs were identified in the 1990s, with a preference for markers in putative gene deserts to avoid forensic profiles revealing protected medical information. We revisit that assumption, investigating whether forensic genetic profiles reveal information about gene-expression variation or potential medical information.

Transplantation of human neural progenitor cells secreting GDNF into the spinal cord of patients with ALS: a phase 1/2a trial.

Amyotrophic lateral sclerosis (ALS) involves progressive motor neuron loss, leading to paralysis and death typically within 3-5 years of diagnosis. Dysfunctional astrocytes may contribute to disease and glial cell line-derived neurotrophic factor (GDNF) can be protective. Here we show that human neural progenitor cells transduced with GDNF (CNS10-NPC-GDNF) differentiated to astrocytes protected spinal motor neurons and were safe in animal models.

Wine yeast selection in the Iberian Peninsula: and non- as drivers of innovation in Spanish and Portuguese wine industries.

Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on , and, lately, with intense activity on non-. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties.

Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines.

Answer ALS is a biological and clinical resource of patient-derived, induced pluripotent stem (iPS) cell lines, multi-omic data derived from iPS neurons and longitudinal clinical and smartphone data from over 1,000 patients with ALS. This resource provides population-level biological and clinical data that may be employed to identify clinical-molecular-biochemical subtypes of amyotrophic lateral sclerosis (ALS). A unique smartphone-based system was employed to collect deep clinical data, including fine motor activity, speech, breathing and linguistics/cognition.

An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients.

Neurodegenerative diseases are challenging for systems biology because of the lack of reliable animal models or patient samples at early disease stages. Induced pluripotent stem cells (iPSCs) could address these challenges. We investigated DNA, RNA, epigenetics, and proteins in iPSC-derived motor neurons from patients with ALS carrying hexanucleotide expansions in .

Improvement of Must Fermentation from Late Harvest cv. Tempranillo Grapes Treated with Pulsed Light.

Pulsed light irradiation is a nonthermal technology currently used for the elimination of pathogens from a diverse range of food products. In the last two decades, the results obtained using PL at laboratory scale are encouraging wine experts to use it in the winemaking industry. PL can reduce native yeast counts significantly, which facilitates the use of starter cultures, reducing SO requirements at the same time.

The history and evolution of the Denisovan- haplotype in Tibetans.

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals.

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations.

The Impact of Fermentation and Ageing on Lees on the Terpenic Aromatic Profile of White Wines of the Albillo Variety.

is a non- yeast that has a powerful impact on the sensory profile of wines. Its effect on the aromatic profile of non-aromatic grape varieties, such as Albillo Mayor (, L), during vinification is a useful biotechnology to improve sensory complexity. Fermentation in steel barrels using and sequential inoculation with have been used to study the formation of terpenes and cell lysis in the production of Albillo white wines.

Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures.

Induced pluripotent stem cell (iPSC)-derived neural cultures from amyotrophic lateral sclerosis (ALS) patients can model disease phenotypes. However, heterogeneity arising from genetic and experimental variability limits their utility, impacting reproducibility and the ability to track cellular origins of pathogenesis. Here, we present methodologies using single-cell RNA sequencing (scRNA-seq) analysis to address these limitations.

Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates.

Since 2015, we have run a free 9-week summer program that provides non-computer science (CS) undergraduates at San Francisco State University (SFSU) with experience in coding and doing research. Undergraduate research experiences remain very limited at SFSU and elsewhere, so the summer program provides opportunities for many more students beyond the mentoring capacity of our university laboratories. In addition, we were concerned that many students from historically underrepresented (HU) groups may be unable to take advantage of traditional summer research programs because these programs require students to relocate or be available full time, which is not feasible for students who have family, work, or housing commitments.

White wine processing by UHPH without SO. Elimination of microbial populations and effect in oxidative enzymes, colloidal stability and sensory quality.

The use of UHPH sterilization in the absence of SO has been used to eliminate wild microorganisms and inactivate oxidative enzymes. A white must of the Muscat of Alexandria grape variety was continuously processed by UHPH at 300 MPa (inlet temperature: 23-25 °C). The initial microbial load of the settled must was 4-log CFU/mL for both yeast and moulds, and slightly lower for bacteria.

Industrial Performance of Several Strains for pH Control in White Wines from Warm Areas.

In the current scenario of climatic warming, the over-ripening of grapes increases the sugar content, producing flat and alcoholic wines with low acidity, high pH and low freshness. Additionally, a high pH makes wines more chemically and microbiologically unstable, requiring a higher sulphite content for preservation. Some strains of can naturally lower the pH of wine by producing lactic acid from sugars; this pH reduction can reach 0.

iPSC modeling of young-onset Parkinson's disease reveals a molecular signature of disease and novel therapeutic candidates.

Young-onset Parkinson's disease (YOPD), defined by onset at <50 years, accounts for approximately 10% of all Parkinson's disease cases and, while some cases are associated with known genetic mutations, most are not. Here induced pluripotent stem cells were generated from control individuals and from patients with YOPD with no known mutations. Following differentiation into cultures containing dopamine neurons, induced pluripotent stem cells from patients with YOPD showed increased accumulation of soluble α-synuclein protein and phosphorylated protein kinase Cα, as well as reduced abundance of lysosomal membrane proteins such as LAMP1.

Contribution of Non- Yeasts to Wine Freshness. A Review.

Freshness, although it is a concept difficult to define in wines, can be understood as a combination of different circumstances. Organolepticwise, bluish red, floral and fruity, more acidic and full-bodied wines, are perceived as younger and fresher by consumers. In traditional winemaking processes, these attributes are hard to boost if no other technology or biotechnology is involved.

Use of fumaric acid to control pH and inhibit malolactic fermentation in wines.

Fumaric acid is an additive allowed by the Codex Alimentarius and under evaluation by the International Organisation of Vine and Wine (OIV) that can be used for wine acidification but also to inhibit malolactic fermentation (MLF). The use of 300-900 mg/L of fumaric acid can inhibit MLF in red wines decreasing pH by 0.2 units or more depending on the buffer capacity.

The study of Positive and Negative Affect in children and adolescents: New advances in a Spanish version of the PANAS.

The study of affective disorders among young population has become increasingly relevant in the last years. The PANAS is a widely used questionnaire devoted to assess positive and negative affect. The main purpose of the current study was to examine the psychometric properties of the Spanish version of the PANAS for children (PANAS).

Detecting inherited and novel structural variants in low-coverage parent-child sequencing data.

Structural variants (SVs) are a class of genomic variation shared by members of the same species. Though relatively rare, they represent an increasingly important class of variation, as SVs have been associated with diseases and susceptibility to some types of cancer. Common approaches to SV detection require the sequencing and mapping of fragments from a test genome to a high-quality reference genome.

Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture.

Bacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms.

Structural Variant Prediction in Extended Pedigrees Through Sparse Negative Binomial Genome Signal Recovery.

Structural variants (SVs) are rearrangements, such as deletions, insertions, duplications, inversions, and translocations, in an individual's genome relative to a reference. SV detection is often marred by high false positive rates due to errors in sequencing and mapping. In previous work, we proposed a maximum likelihood approach to SV prediction that incorporated low-coverage sequencing data and coverage distribution.

Modeling transposable element dynamics with fragmentation equations.

Transposable elements (TEs), segments of DNA capable of self-replication, are abundant in the genomes of most organisms and thus serve as a record of past mutational events. While some work suggests TEs may serve a regulatory function for the host, most empirical and theoretical studies have shown that TEs often have deleterious effects on a host. Because they are not essential, the host genome consists of both full-length (actively replicating) and partial length (inactive remnant) copies of TEs.