Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.

Many subtypes of cortical interneurons (CINs) are found in adult mouse cortices, but the mechanism generating their diversity remains elusive. We performed single-cell RNA sequencing on the mouse embryonic medial ganglionic eminence (MGE), the major birthplace for CINs, and on MGE-like cells differentiated from embryonic stem cells. Two distinct cell types were identified as proliferating neural progenitors and immature neurons, both of which comprised sub-populations. Although lineage development of MGE progenitors was reconstructed and immature neurons were characterized as GABAergic, cells that might correspond to precursors of different CINs were not identified. A few non-neuronal cell types were detected, including microglia. In vitro MGE-like cells resembled bona fide MGE cells but expressed lower levels of Foxg1 and Epha4. Together, our data provide detailed understanding of the embryonic MGE developmental program and suggest how CINs are specified

Effect of short-term bee bread on testicular cell development and testosterone level in male Sprague Dawley rats

Bee bread has been widely traditionally used for male fertility enrichment although limited scientific data are available on its effectiveness. Hence, the aim of this study was to determine the effect of bee bread on testicular cell development and testosterone level in male Sprague Dawley rats. In this study, 24 adult male Sprague-Dawley rats were selected and divided equally into four treatment groups (n = 6/group) which were Control (C: 0 g of bee bread/kg body weight), Treatment 1 (T1: 1 g of bee bread /kg body weight), Treatment 2 (T2: 2 g of bee bread /kg body weight) and Treatment 3 (T3: 3 g of bee bread /kg body weight). The bee bread was administered daily and orally according to the designated treatment groups using oral gavage for 28 days. After 28 days of treatment, rats were euthanised and testicular cell development and testosterone level were measured. Results showed that rats in the T2 group had thicker (P<0.05) seminiferous tubular diameter (STD) than the control group and higher (P<0.05) seminiferous epithelial height (SEH) compared to C and T1 groups. The testosterone level in the T1, T2 and T3 groups was significantly higher (P<0.05) compared to control. In conclusion, this study suggests that supplemented with 2 g of bee bread per kg body weight is likely to give a positive effect by improving testicular cells development and testosterone level in male Sprague Dawley rats

Skeletal Deformities in Cultured Juvenile African Catfish Clarias gariepinus (Burchell, 1822)

Skeletal deformities in cultured fish are known worldwide and it had affected the survival, growth and appearance of the fish which contribute to production loss. Clarias gariepinus is known as number one farmed fish in Malaysia. C. gariepinus also effected in these deformities especially in cultured species. The objectives of this study are to identify the skeletal deformities that occur in juvenile stages and to compare the bone structure between the normal and deformed fish. A total of 50 juveniles’ fish were collected from Aquaculture Extension and Community Centre Machang, Kelantan. The juvenile was measured before undergo staining process. The fish were starved for one day then fixed in 70% ethanol for two weeks. The fish were then stained with alizarin red S for cartilage and Alcian blue for bone. The specimens were photographed in order to observe the deformities. The data showed only 13.0% juveniles have skeletal deformities, 10.9% with lordosis and 2.2% scoliosis. The cause of the deformities may be due to the heterogenous growth but other factors might also contribute to the problem. As the conclusion, the skeletal deformities observed in juvenile C. gariepinus were detected with the whole-mount staining method ranged from size 7.3 and 26.0 cm in total length. This study shows there is heterogenous growth rearing at low percentage even from skilled farm. Further study should concentrate on hidden factors that affected the deformity rate and mineralization of the juvenile fish

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

This research was carried out within the framework of the DREAM Community of Premature Births, of which UDC researchers Diego Fernández-Edreira and Carlos Fernández-Lozano, who have collaborated in the research, are members.Supplementary research data are available at https://www.cell.com/cms/10.1016/j.xcrm.2023.101350/attachment/e44bcada-f500-4f17-bc33-0ee5d39b3c4b/mmc1.pdf.[Abstract]: Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth.We thank members of the Sirota Lab, University of California, San Francisco, for useful discussion. This study was supported by the March of Dimes (J.L.G., T.T.O., A.R., A.S.T., V.C., C.W.Y.H., R.J.W., K.J.F., G.A., I.K., J.B., A.N., J.G., Z.W., P.N., A.K., I.B., E.K., S.J., S.N., Y.S.L., P.R.B., D.A.M., S.V.L., J.A., D.K.S., N.Aghaeepour, J.C.C., M.S.) and R35GM138353 (N.Aghaeepour), 1R01HL139844 (N.Aghaeepour), 3P30AG066515 (N.Aghaeepour), 1R61NS114926 (N.Aghaeepour), 1R01AG058417 (N.Aghaeepour), R01HD105256 (N.Aghaeepour, M.S.), P01HD106414 (N.Aghaeepour), R01GM140464 (J.G., Z.W., G.C., Z.-Z.T.), NSF DMS-2054346 (J.G., Z.W., G.C., Z.-Z.T.); the Burroughs Welcome Fund (N.Aghaeepour); the Alfred E. Mann Foundation (N.Aghaeepour); and the Robertson Foundation (N.Aghaeepour). A.P.-L. and P.D.-G. are receiving honoraria from the IVI Foundation.United States. National Institute of General Medical Sciences; R35GM138353United States. National Institutes of Health; 1R01HL139844United States. National Institutes of Health; 3P30AG066515United States. National Institutes of Health; 1R61NS114926United States. National Institute on Aging; 1R01AG058417United States. National Institute of Child Health and Human Development; R01HD105256United States. National Institute of Child Health and Human Development; P01HD106414United States. National Institutes of Health; R01GM140464United States. National Science Foundation; DMS-205434

A simple DNA stretching method for fluorescence imaging of single DNA molecules

Stretching or aligning DNA molecules onto a surface by means of molecular combing techniques is one of the critical steps in single DNA molecule analysis. However, many of the current studies have focused on λ-DNA, or other large DNA molecules. There are very few studies on stretching methodologies for DNA molecules generated via PCR (typically smaller than 20 kb). Here we describe a simple method of stretching DNA molecules up to 18 kb in size on a modified glass surface. The very low background fluorescence allows efficient detection of single fluorescent dye labels incorporated into the stretched DNA molecules

Rapid DNA mapping by fluorescent single molecule detection

DNA mapping is an important analytical tool in genomic sequencing, medical diagnostics and pathogen identification. Here we report an optical DNA mapping strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs on the molecules. Individual genomic DNA molecules were labeled with fluorescent dyes at specific sequence motifs by the action of nicking endonuclease followed by the incorporation of dye terminators with DNA polymerase. The labeled DNA molecules were then stretched into linear form on a modified glass surface and imaged using total internal reflection fluorescence (TIRF) microscopy. By determining the positions of the fluorescent labels with respect to the DNA backbone, the distribution of the sequence motif recognized by the nicking endonuclease can be established with good accuracy, in a manner similar to reading a barcode. With this approach, we constructed a specific sequence motif map of lambda-DNA. We further demonstrated the capability of this approach to rapidly type a human adenovirus and several strains of human rhinovirus

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; \u3c37 \u3eweeks) or (2) early preterm birth (ePTB; \u3c32 \u3eweeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth

Characterization of Avian Influenza Viruses A (H5N1) from Wild Birds, Hong Kong, 2004–2008

Repeated detection of subclade 2.3.2 viruses in nonpasserine birds from different regions suggests possible establishment of this lineage in wild bird species

Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA)

<p>Abstract</p> <p>Background</p> <p>Prospective typing of <it>Salmonella enterica </it>serovar Typhimurium (STM) by multiple-locus variable-number tandem-repeat analysis (MLVA) can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the dynamics of human STM infection in a prospective study of STM MLVA typing for public health surveillance.</p> <p>Methods</p> <p>During a three-year period between August 2007 and September 2010 all confirmed STM isolates were fingerprinted using MLVA as part of the New South Wales (NSW) state public health surveillance program.</p> <p>Results</p> <p>A total of 4,920 STM isolates were typed and a subset of 4,377 human isolates was included in the analysis. The STM spectrum was dominated by a small number of phage types, including DT170 (44.6% of all isolates), DT135 (13.9%), DT9 (10.8%), DT44 (4.5%) and DT126 (4.5%). There was a difference in the discriminatory power of MLVA types within endemic phage types: Simpson's index of diversity ranged from 0.109 and 0.113 for DTs 9 and 135 to 0.172 and 0.269 for DTs 170 and 44, respectively. 66 distinct STM clusters were observed ranging in size from 5 to 180 cases and in duration from 4 weeks to 25 weeks. 43 clusters had novel MLVA types and 23 represented recurrences of previously recorded MLVA types. The diversity of the STM population remained relatively constant over time. The gradual increase in the number of STM cases during the study was not related to significant changes in the number of clusters or their size. 667 different MLVA types or patterns were observed.</p> <p>Conclusions</p> <p>Prospective MLVA typing of STM allows the detection of community outbreaks and demonstrates the sustained level of STM diversity that accompanies the increasing incidence of human STM infections. The monitoring of novel and persistent MLVA types offers a new benchmark for STM surveillance.</p> <p>A part of this study was presented at the MEEGID × (Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) Conference, 3-5 November 2010, Amsterdam, The Netherlands</p