The Need for Positive Behavior Supports in Schools

Student misbehavior can be a hindrance to the educational process in a school. Undesirable behavior may distract pupils from a lesson, teachers from instruction, administrators from other duties, and the offender from his or her own learning. Often, a misbehaving student is removed from the classroom or school building. This approach to managing student behavior is not effective in the long term, as studies show individuals do not benefit from exclusion from instruction. Adults in a school building must look into ways to support students in learning how to behave appropriately. In addition to clearly communicated behavioral expectations and consequences, school personnel should provide various support structures to students: beforeand after-school programs, counselors, clubs and activities, social-skills training, educational sanctions, and the like. Additionally, building adults must share a commitment to consistent enforcement of school policy within their respective domains

Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides

Variation in RNA splicing (i.e., alternative splicing) plays an important role in many diseases. Variants near 5' and 3' splice sites often affect splicing, but the effects of these variants on splicing and disease have not been fully characterized beyond the two "essential" splice nucleotides flanking each exon. Here we provide quantitative measurements of tolerance to mutational disruptions by position and reference allele-alternative allele combinations. We show that certain reference alleles are particularly sensitive to mutations, regardless of the alternative alleles into which they are mutated. Using public RNA-seq data, we demonstrate that individuals carrying such variants have significantly lower levels of the correctly spliced transcript, compared to individuals without them, and confirm that these specific substitutions are highly enriched for known Mendelian mutations. Our results propose a more refined definition of the "splice region" and offer a new way to prioritize and provide functional interpretation of variants identified in diagnostic sequencing and association studies.Peer reviewe

Quantifying unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects

As new proposals aim to sequence ever larger collection of humans, it is critical to have a quantitative framework to evaluate the statistical power of these projects. We developed a new algorithm, UnseenEst, and applied it to the exomes of 60,706 individuals to estimate the frequency distribution of all protein-coding variants, including rare variants that have not been observed yet in the current cohorts. Our results quantified the number of new variants that we expect to identify as sequencing cohorts reach hundreds of thousands of individuals. With 500K individuals, we find that we expect to capture 7.5% of all possible loss-of-function variants and 12% of all possible missense variants. We also estimate that 2,900 genes have loss-of-function frequency of <0.00001 in healthy humans, consistent with very strong intolerance to gene inactivation.United States. National Institutes of Health (U54DK105566)United States. National Institutes of Health (R01GM104371

Differences in Relative Abundance of GnRH-I and GnRH-II in Granulosa Cells of Bovine Antral Follicles at Specific Stages of Follicular Development

Increased estradiol is the primary signal to initiate standing estrus, and cows that exhibit estrus prior to fixed-time artificial insemination have greater pregnancy rates than cows that do not. Therefore, understanding what factors may be present at the ovary that may regulate estradiol production is critical. A previous study reported that bovine follicles with greater follicular fluid concentrations of estradiol had decreased expression of GnRH-I and GnRH-II in granulosa cells (GC). The objective of this study was to characterize relative abundance of GnRH-I and -II mRNA within GC of follicles at specific stages of development. Beef cows were synchronized, and ovaries were collected at specific stages of follicular development [pre-selection (PRE), post-selection (POST), and post-selection 24 h after luteal regression (POST-PG)]. All surface follicles were classified as small (\u3c 5mm), medium (5 - 8mm), or large (\u3e 8mm) and aspirated to collect GC. Large follicles from each animal were kept separate and all other follicles were pooled by size within animal (n = 27, 27, and 18 for small, medium, and large). Total cellular RNA was extracted, and RT-PCR was performed for GnRH-I, GnRH-II, and GAPDH. Data were analyzed using the MIXED procedure of SAS. Across all follicles, GnRH-I and GnRH-II expression were not influenced by stage (P = 0.27) but were influenced by size (P \u3c 0.01). Smalls (4.55 ± 0.39 and 3.91 ± 0.44, respectively) had greater expression (P ≤ 0.01) of GnRH compared to mediums (0.83 ± 0.39 and 1.41 ± 0.44, respectively) and larges (0.52 ± 0.47 and 2.12 ± 0.54, respectively). There was also a stage by size interaction (P \u3c 0.01). POST (P \u3c 0.01) and POST-PG (P ≤ 0.08) smalls had or tended to have increased expression compared to PRE smalls, but PRE mediums had increased expression (P \u3c 0.03) compared to POST-PG mediums. When only the largest follicle for each animal was evaluated, stage of development influenced expression of GnRH-I (P = 0.03) but not GnRH-II (P = 0.91). For GnRH-I, PRE tended (P = 0.09; 2.29 ± 0.55) to have increased expression compared to POST (0.92 ± 0.55) and did have greater expression compared to POST-PG (P = 0.01; 0.11 ± 0.55). Thus, GnRH within antral follicles may be a key regulator of the follicle’s ability to produce estradiol

Influence of Bovine Viral Diarrhea Virus Infection on Artificial Insemination Conception and Breeding Season Pregnancy Success in Vaccinated Beef Herds

Bovine Viral Diarrhea Virus (BVDV) causes reproductive economic losses in cattle. The objective of this study was to evaluate the influence of BVDV infection on reproductive success. Vaccinated cows (n = 370) and heifers (n = 528) from nine different herds were synchronized using the 7-day CO-Synch + CIDR protocol and were bred using fixed-time artificial insemination (FTAI). On d 28 following insemination, blood samples were collected and pregnancy status was determined. Non-pregnant animals were resynchronized and FTAI occurred a second time. In six herds, bulls were comingled with females beginning 10-15 d after the second AI. Final pregnancy status was determined 33-80 d following the first pregnancy diagnosis. Blood samples were tested for the presence of BVDV antigen using the IDEXX BVDV PI X2 Kit. Animals that tested positive were considered infected with BVDV at the time of blood collection. Herds were determined to be BVDV infected by the presence of at least one animal having a positive test for antigen (n = 4 infected herds, n = 5 non-infected herds). Statistical analyses were performed using the GLIMMIX procedure of SAS with herd as a random variable. Herds that had evidence of BVDV infection at d 28 following insemination had significantly decreased (P \u3c 0.01) first service AI conception rates compared to herds that had no evidence of infection (34 ± 2.3% vs. 54 ± 2.3%, respectively). Additionally, breeding season pregnancy rates were decreased (P \u3c 0.01) in BVDV infected herds compared to non-infected herds (69 ± 3.4% vs. 80 ± 3.6%, respectively). There was no significant effect of BVDV infection status on embryonic loss (P = 0.42) or percentage of animals which lost a pregnancy and rebred by the end of the breeding season (P = 0.63). In conclusion, BVDV infection in well vaccinated herds had a significant negative impact on both first service AI conception rate and overall breeding season pregnancy success

A framework for the detection of de novo mutations in family-based sequencing data

Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants and short insertions and deletions (indels) from sequence data collected in parent-offspring trios. We compute the joint probability of the data given the genotype likelihoods in the individual family members, the known familial relationships and a prior probability for the mutation rate. Candidate de novo mutations (DNMs) are reported along with their posterior probability, providing a systematic way to prioritize them for validation. Our tool is integrated in the Genome Analysis Toolkit and can be used together with the ReadBackedPhasing module to infer the parental origin of DNMs based on phase-informative reads. Using simulated data, we show that PBT outperforms existing tools, especially in low coverage data and on the X chromosome. We further show that PBT displays high validation rates on empirical parent-offspring sequencing data for whole-exome data from 104 trios and X-chromosome data from 249 parent-offspring families. Finally, we demonstrate an association between father's age at conception and the number of DNMs in female offspring's X chromosome, consistent with previous literature reports

Mosaic fungal individuals have the potential to evolve within a single generation

Although cells of mushroom-producing fungi typically contain paired haploid nuclei (n + n), most Armillaria gallica vegetative cells are uninucleate. As vegetative nuclei are produced by fusions of paired haploid nuclei, they are thought to be diploid (2n). Here we report finding haploid vegetative nuclei in A. gallica at multiple sites in southeastern Massachusetts, USA. Sequencing multiple clones of a single-copy gene isolated from single hyphal filaments revealed nuclear heterogeneity both among and within hyphae. Cytoplasmic bridges connected hyphae in field-collected and cultured samples, and we propose nuclear migration through bridges maintains this nuclear heterogeneity. Growth studies demonstrate among- and within-hypha phenotypic variation for growth in response to gallic acid, a plant-produced antifungal compound. The existence of both genetic and phenotypic variation within vegetative hyphae suggests that fungal individuals have the potential to evolve within a single generation in response to environmental variation over time and space

A framework for the detection of de novo mutations in family-based sequencing data

Francioli LC, Cretu-Stancu M, Garimella KV, et al. A framework for the detection of de novo mutations in family-based sequencing data. European Journal of Human Genetics. 2016;25(2):227-233