18 research outputs found
Relationship of depressive symptomatology and academic achievement motivation in the school to the social responses of teachers
Widespread Genomic Signatures of Natural Selection in Hominid Evolution
Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19β26% on the autosomes and 12β40% on the X chromosome. The overall trends are broadly consistent with βbackground selectionβ or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events
The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist
Fibrobacter succinogenes is an important member of the rumen
microbial community that converts plant biomass into nutrients usable by its
host. This bacterium, which is also one of only two cultivated species in its
phylum, is an efficient and prolific degrader of cellulose. Specifically, it has
a particularly high activity against crystalline cellulose that requires close
physical contact with this substrate. However, unlike other known cellulolytic
microbes, it does not degrade cellulose using a cellulosome or by producing high
extracellular titers of cellulase enzymes. To better understand the biology of
F. succinogenes, we sequenced the genome of the type strain
S85 to completion. A total of 3,085 open reading frames were predicted from its
3.84 Mbp genome. Analysis of sequences predicted to encode for
carbohydrate-degrading enzymes revealed an unusually high number of genes that
were classified into 49 different families of glycoside hydrolases, carbohydrate
binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of
the 31 identified cellulases, none contain CBMs in families 1, 2, and 3,
typically associated with crystalline cellulose degradation. Polysaccharide
hydrolysis and utilization assays showed that F. succinogenes
was able to hydrolyze a number of polysaccharides, but could only utilize the
hydrolytic products of cellulose. This suggests that F.
succinogenes uses its array of hemicellulose-degrading enzymes to
remove hemicelluloses to gain access to cellulose. This is reflected in its
genome, as F. succinogenes lacks many of the genes necessary to
transport and metabolize the hydrolytic products of non-cellulose
polysaccharides. The F. succinogenes genome reveals a bacterium
that specializes in cellulose as its sole energy source, and provides insight
into a novel strategy for cellulose degradation
Targeted discovery of novel human exons by comparative genomics
A complete and accurate set of human protein-coding gene annotations is perhaps the single most important resource for genomic research after the human-genome sequence itself, yet the major gene catalogs remain incomplete and imperfect. Here we describe a genome-wide effort, carried out as part of the Mammalian Gene Collection (MGC) project, to identify human genes not yet in the gene catalogs. Our approach was to produce gene predictions by algorithms that rely on comparative sequence data but do not require direct cDNA evidence, then to test predicted novel genes by RTβPCR. We have identified 734 novel gene fragments (NGFs) containing 2188 exons with, at most, weak prior cDNA support. These NGFs correspond to an estimated 563 distinct genes, of which >160 are completely absent from the major gene catalogs, while hundreds of others represent significant extensions of known genes. The NGFs appear to be predominantly protein-coding genes rather than noncoding RNAs, unlike novel transcribed sequences identified by technologies such as tiling arrays and CAGE. They tend to be expressed at low levels and in a tissue-specific manner, and they are enriched for roles in motor activity, cell adhesion, connective tissue, and central nervous system development. Our results demonstrate that many important genes and gene fragments have been missed by traditional approaches to gene discovery but can be identified by their evolutionary signatures using comparative sequence data. However, they suggest that hundredsβnot thousandsβof protein-coding genes are completely missing from the current gene catalogs
The Relationship of Parental Overprotection and Perceived Child Vulnerability to Depressive Symptomotology in Children With Type 1 Diabetes Mellitus: The Moderating Influence of Parenting Stress
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Human-specific NOTCH2NL genes affect notch signaling and cortical neurogenesis
Genetic changes causing brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and is a determinant of neuronal number in the mammalian cortex. We find that three paralogs of human-specific NOTCH2NL are highly expressed in radial glia. Functional analysis reveals that different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation into cortical neurons. Furthermore, NOTCH2NL genes provide the breakpoints in 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism and deletions with microcephaly and schizophrenia. Thus, the emergence of human-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger human neocortex, accompanied by loss of genomic stability at the 1q21.1 locus and resulting recurrent neurodevelopmental disorders