Explore the vast range of titles available.

Background Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging. Results Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3′ shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation. Conclusion The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility. Graphical abstract

Genetic mechanisms underlying abnormal early neural development in toddlers with Autism Spectrum Disorder (ASD) remain uncertain due to the impossibility of direct brain gene expression measurement during critical periods of early development. Recent findings from a multi‐tissue study demonstrated high expression of many of the same gene networks between blood and brain tissues, in particular with cell cycle functions. We explored relationships between blood gene expression and total brain volume (TBV) in 142 ASD and control male toddlers. In control toddlers, TBV variation significantly correlated with cell cycle and protein folding gene networks, potentially impacting neuron number and synapse development. In ASD toddlers, their correlations with brain size were lost as a result of considerable changes in network organization, while cell adhesion gene networks significantly correlated with TBV variation. Cell cycle networks detected in blood are highly preserved in the human brain and are upregulated during prenatal states of development. Overall, alterations were more pronounced in bigger brains. We identified 23 candidate genes for brain maldevelopment linked to 32 genes frequently mutated in ASD. The integrated network includes genes that are dysregulated in leukocyte and/or postmortem brain tissue of ASD subjects and belong to signaling pathways regulating cell cycle G1/S and G2/M phase transition. Finally, analyses of the CHD8 subnetwork and altered transcript levels from an independent study of CHD8 suppression further confirmed the central role of genes regulating neurogenesis and cell adhesion processes in ASD brain maldevelopment. Synopsis Analyses of the relationship between blood gene expression and brain size in 142 Autism Spectrum Disorder (ASD) and control male toddlers reveal peripheral blood signatures of ASD and genetic mechanisms underlying abnormal early neural development. In ASD, the correlation of brain size measures with cell cycle and protein folding gene networks is lost, while cell adhesion networks significantly correlate with brain size. Cell cycle networks detected in blood are highly preserved in the human brain and are upregulated during prenatal states of development. In ASD, cell cycle networks display changes in topological organization and these alterations are more pronounced in bigger brains. A predicted high‐confidence network indicates dysregulation of neurogenesis and cell adhesion processes in ASD brain development. Graphical Abstract Analyses of the relationship between blood gene expression and brain size in 142 Autism Spectrum Disorder (ASD) and control male toddlers reveal peripheral blood signatures of ASD and genetic mechanisms underlying abnormal early neural development.

The wave–particle duality is the quintessence of quantum mechanics. This duality gives rise to distinct behaviors depending on the experimental setup, with the system exhibiting either wave-like or particle-like properties, depending on whether the focus is on interference (wave) or trajectory (particle). In the interaction with a beam splitter, photons with particle behavior can transform into a wave behavior and vice versa. In Wheeler’s delayed-choice gedanken experiment, this interaction is delayed so that the wave that initially travels through the interferometer can become a particle, avoiding the interaction. We show that this contradiction can be resolved using polarized entangled photon pairs. An analysis of Shannon’s entropy supports this proposal.

Growth in international migration is attributable to conflicts and war, food insecurity, violence, and lack of economic opportunity. Additionally, according to the World Bank, the world could see more than 140 million people move within countries by 2050, and many expect that climate change will lead to even greater migration and displacement. Cities are on the front lines in creating innovative policy and programs to integrate immigrants, refugees, and asylum seekers. Los Angeles has developed programs and policies to ensure that newcomers have the opportunity to thrive economically, civically, and to obtain key city services such as healthcare and financial support. This article examines a few innovative models aimed at addressing integration for migrant and refugee populations in L.A. and provides recommendations for how cities can replicate these models.

Background Social affective and communication symptoms are central to autism spectrum disorder (ASD), yet their severity differs across toddlers: Some toddlers with ASD display improving abilities across early ages and develop good social and language skills, while others with “profound” autism have persistently low social, language and cognitive skills and require lifelong care. The biological origins of these opposite ASD social severity subtypes and developmental trajectories are not known. Methods Because ASD involves early brain overgrowth and excess neurons, we measured size and growth in 4910 embryonic-stage brain cortical organoids (BCOs) from a total of 10 toddlers with ASD and 6 controls (averaging 196 individual BCOs measured/subject). In a 2021 batch, we measured BCOs from 10 ASD and 5 controls. In a 2022 batch, we  tested replicability of BCO size and growth effects by generating and measuring an independent batch of BCOs from 6 ASD and 4 control subjects. BCO size was analyzed within the context of our large, one-of-a-kind social symptom, social attention, social brain and social and language psychometric normative datasets ranging from N = 266 to N = 1902 toddlers. BCO growth rates were examined by measuring size changes between 1- and 2-months of organoid development. Neurogenesis markers at 2-months were examined at the cellular level. At the molecular level, we measured activity and expression of Ndel1; Ndel1 is a prime target for cell cycle-activated kinases; known to regulate cell cycle, proliferation, neurogenesis, and growth; and known to be involved in neuropsychiatric conditions. Results At the BCO level, analyses showed BCO size was significantly enlarged by 39% and 41% in ASD in the 2021 and 2022 batches. The larger the embryonic BCO size, the more severe the ASD social symptoms. Correlations between BCO size and social symptoms were r = 0.719 in the 2021 batch and r = 0. 873 in the replication 2022 batch. ASD BCOs grew at an accelerated rate nearly 3 times faster than controls. At the cell level, the two largest ASD BCOs had accelerated neurogenesis. At the molecular level, Ndel1 activity was highly correlated with the growth rate and size of BCOs. Two BCO subtypes were found in ASD toddlers: Those in one subtype had very enlarged BCO size with accelerated rate of growth and neurogenesis; a profound autism clinical phenotype displaying severe social symptoms, reduced social attention, reduced cognitive, very low language and social IQ; and substantially altered growth in specific cortical social, language and sensory regions. Those in a second subtype had milder BCO enlargement and milder social, attention, cognitive, language and cortical differences. Limitations Larger samples of ASD toddler-derived BCO and clinical phenotypes may reveal additional ASD embryonic subtypes. Conclusions By embryogenesis, the biological bases of two subtypes of ASD social and brain development—profound autism and mild autism—are already present and measurable and involve dysregulated cell proliferation and accelerated neurogenesis and growth. The larger the embryonic BCO size in ASD, the more severe the toddler’s social symptoms and the more reduced the social attention, language ability, and IQ, and the more atypical the growth of social and language brain regions.

The sense of smell plays a fundamental role in mammalian survival. There is a considerable amount of information available on the vomeronasal system of both domestic and wild canids. However, much less information is available on the canid main olfactory system, particularly at the level of the main olfactory bulb. Comparative study of the neuroanatomy of wild and domestic canids provides an excellent model for understanding the effects of selection pressure associated with domestication. A comprehensive histological (hematoxylin–eosin, Nissl, Tolivia and Gallego’s Trichrome stains), lectin (UEA, LEA) and immunohistochemical (Gαo, Gαi2, calretinin, calbindin, olfactory marker protein, glial fibrillary acidic protein, microtubule-associated protein 2) study of the olfactory bulbs of the dog, fox and wolf was performed. Our study found greater macroscopic development of the olfactory bulb in both the wolf and fox compared to the dog. At the microscopic level, all three species show a well-developed pattern of lamination and cellularity typical of a macrosmatic animal. However, greater development of cellularity in the periglomerular and mitral layers of wild canids is characteristic. Likewise, the immunohistochemical study shows comparable results between the three species, but with a noticeably higher expression of markers in wild canids. These results suggest that the reduction in encephalization experienced in dogs due to domestication also corresponds to a lower degree of morphological and neurochemical differentiation of the olfactory bulb.

Mucin type O-glycosylation is one of the most common types of post-translational modifications that impacts stability and biological functions of many mammalian proteins. A large family of UDP-GalNAc polypeptide:N-acetyl-α-galactosaminyltransferases (GalNAc-Ts) catalyzes the first step of mucin type O-glycosylation by transferring GalNAc to serine and/or threonine residues of acceptor polypeptides. Plants do not have the enzyme machinery to perform this process, thus restricting their use as bioreactors for production of recombinant therapeutic proteins. The present study demonstrates that an isoform of the human GalNAc-Ts family, GalNAc-T2, retains its localization and functionality upon expression in N. benthamiana L. plants. The recombinant enzyme resides in the Golgi as evidenced by the fluorescence distribution pattern of the GalNAc-T2:GFP fusion and alteration of the fluorescence signature upon treatment with Brefeldin A. A GalNAc-T2-specific acceptor peptide, the 113-136 aa fragment of chorionic gonadotropin β-subunit, is glycosylated in vitro by the plant-produced enzyme at the \"native\" GalNAc attachment sites, Ser-121 and Ser-127. Ectopic expression of GalNAc-T2 is sufficient to \"arm\" tobacco cells with the ability to perform GalNAc-glycosylation, as evidenced by the attachment of GalNAc to Thr-119 of the endogenous enzyme endochitinase. However, glycosylation of highly expressed recombinant glycoproteins, like magnICON-expressed E. coli enterotoxin B subunit:H. sapiens mucin 1 tandem repeat-derived peptide fusion protein (LTBMUC1), is limited by the low endogenous UDP-GalNAc substrate pool and the insufficient translocation of UDP-GalNAc to the Golgi lumen. Further genetic engineering of the GalNAc-T2 plants by co-expressing Y. enterocolitica UDP-GlcNAc 4-epimerase gene and C. elegans UDP-GlcNAc/UDP-GalNAc transporter gene overcomes these limitations as indicated by the expression of the model LTBMUC1 protein exclusively as a glycoform. Plant bioreactors can be engineered that are capable of producing Tn antigen-containing recombinant therapeutics.

Do you want to make an impact in the community that your library serves? Are you struggling with comparing your work to your peers, or feeling like you aren't doing enough? Everyone wants to feel like their work makes a difference. Two years ago, they were hired to do the same job, in the same public library system, around the same time and at two different branch locations. They navigated their day-to-day duties and fell into routines that made sense for them. But when they compared their days, they looked nothing alike.

Viscera of marine resources represent roughly 10-20% of the total specimen weight and should be studied for utilization in the food industry. In this study, a protein concentrate (PC) was obtained from the viscera of jumbo squids (Dosidicus gigas). Protein fractionation of the viscera material yielded 45.08 ±2.09% sarcoplasmic protein, 38.91 ±0.07% myofibrillar protein and 10.27 ±0.18% alkali-soluble proteins, while the PC showed values of 29.53 ±0.17, 51.20 ±0.75% and 15.92 ±0.15%, respectively. The electrophoretic pattern showed the presence of high molecular weight aggregates and sarcoplasmic proteins and/or hydrolyzed proteins of different molecular weights in both systems. It was possible to obtain gels of protein from viscera, but it was not possible to do so from PC. Viscera and PC were not significantly different (p≥0.05) in emulsification capacity, but the former was more stable; it also showed better foaming capacity than PC, but no difference (p≥0.05) was detected in the foam stability. The results indicate that the proteins present in the viscera of jumbo squid have low-quality gelling properties, but proteins of this by-product showed good emulsification and foam properties, which could be exploited in the production of food or food ingredients intended for human consumption.

Mangrove forests are biodiversity hotspots that provide critical ecosystem services, from coastal protection to carbon storage. Yet, these ecosystems are disappearing at alarming rates, and while restoration efforts are expanding globally, long-term monitoring—especially in the Americas—remains scarce and often narrowly focused on vegetation structure, overlooking biological recovery. In this study, we evaluate whether gastropod community assemblages can serve as functional indicators of ecological recovery across different stages of mangrove restoration in Costa Rica. Using a space-for-time approach, we compared tree structure and gastropod assemblages across restored sites of varying ages, unrestored areas, and mature mangrove forests. We applied linear mixed models to examine how restoration stages influenced structure (tree height and DBH) and biodiversity metrics (gastropod abundance and composition). Tree structure improved consistently with restoration age, with five-year-old trees reaching nearly half the height and DBH of mature forest counterparts. Gastropod abundance exhibited a non-linear response—initially declining post-planting, then peaking by year five. Community composition also shifted: Melampus dominated early stages, while older sites supported Vitta , Cerithideopsis , and Littoraria . The exclusive presence of Thaisella in mature forests suggests its potential as a bioindicator of late-stage ecological recovery. Our results underscore the value of integrating biological indicators into mangrove monitoring. Gastropod assemblages offer a powerful lens through which to monitor ecological functionality, providing a low-cost, scalable tool to enhance adaptive management and guide future restoration efforts in tropical coastal ecosystems.