Recently, students and faculty have been forced to deal with unprecedented disruptions to their courses and broader uncertainties that have presented serious challenges to quality instruction. We ...present a flexible, team-based approach to teaching and learning that can transition seamlessly between face-to-face, hybrid, and fully online instruction when disruptions occur. We have built a community genome annotation program that can be implemented as a module in a biology course, as an entire course, or as directed research projects. This approach maintains an engaging and supportive educational environment and provides students the opportunity to learn and contribute to science with undergraduate research. Students are provided guidance through multiple interactions with faculty and peer mentors to support their progress and encourage learning. Integration of the developed instructional tools with available technology ensures that students can contribute remotely. Through this process, students seamlessly continue their annotation coursework, participate in undergraduate research, and prepare abstracts and posters for virtual conferences. Importantly, this strategy does not impose any additional burden or workload on students, who may already be overwhelmed with the additional work associated with the transition to remote learning. Here, we present tips for implementing this instructional platform, provide an overview of tools that facilitate instruction, and discuss expected educational outcomes.
Hox genes and their cofactors are essential developmental genes specifying regional identity in animals. Hox genes have a conserved arrangement in clusters in the same order in which they specify ...identity along the anterior-posterior axis. A few insect species have breaks in the cluster, but these are exceptions. We annotated the 10 Hox genes of the Asian citrus psyllid
, and found a split in its Hox cluster between the
and
genes - the first time a break at this position has been observed in an insect Hox cluster. We also annotated
orthologs of the Hox cofactor genes
and
and found an additional copy of
in
that appears to be a retrogene. Expression data and sequence conservation suggest that the
retrogene may have retained the original
function and allowed divergence of the parental
gene.
Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases ...required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods. The Asian citrus psyllid,
, carries the bacterium causing Huanglongbing, or citrus greening disease, a devastating citrus disease. We identified and annotated 12 chitinase family genes from
as part of a community effort to create high-quality gene models to aid the design of interdictory molecules for pest control. We categorized the
chitinases according to an established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases from known groups, we identified a novel class of chitinases present in
and several related hemipterans that appears to be the result of horizontal gene transfer.
The polysaccharide chitin is critical for the formation of many insect structures, including the exoskeleton, and is required for normal development. Here we report the annotation of three genes from ...the chitin synthesis pathway in the Asian citrus psyllid,
(Hemiptera: Liviidae), the vector of Huanglongbing (citrus greening disease). Most insects have two chitin synthase (CHS) genes but, like other hemipterans,
has only one. In contrast,
is unusual among insects in having two UDP-N-acetylglucosamine pyrophosphorylase (UAP) genes. One of the
UAP genes is broadly expressed, while the other is expressed predominantly in males. Our work helps pave the way for potential utilization of these genes as pest control targets to reduce the spread of Huanglongbing.
Insects have a segmented body plan that is established during embryogenesis when the anterior-posterior (A-P) axis is divided into repeated units by a cascade of gene expression. The cascade is ...initiated by protein gradients created by translation of maternally provided mRNAs, localized at the anterior and posterior poles of the embryo. Combinations of these proteins activate specific gap genes to divide the embryo into distinct regions along the anterior-posterior axis. Gap genes then activate pair-rule genes, which are usually expressed in parts of every other segment. The pair-rule genes, in turn, activate expression of segment polarity genes in a portion of each segment. The segmentation genes are generally conserved among insects, although there is considerable variation in how they are deployed. We annotated 25 segmentation gene homologs in the Asian citrus psyllid,
. Most of the genes expected to be present in
based on their phylogenetic distribution in other insects were identified and annotated. Two exceptions were
and
, which are present in at least some hemipterans, but were not found in
. Many of the segmentation pathway genes are likely to be essential for
development, and thus they may be useful targets for gene-based pest control methods.
The hemipteran insect
, or Asian citrus psyllid, is a vector for
Liberibacter asiaticus (
Las), the bacterium causing citrus greening disease, or Huanglongbing (HLB). Millions of citrus trees have ...been destroyed, and every grove in Florida, USA, has been directly affected by this disease. In eukaryotes, vacuolar-type ATP synthase (V-ATPase) is an abundant heterodimeric enzyme that serves the cell with essential compartment acidification through the active processes that transport protons across the membrane. Fifteen putative
genes in the
genome were manually curated. Comparative genomic analysis revealed that
V-ATPase subunits share domains and motifs with other insects, including the V-ATPase-A superfamily domain. Phylogenetic analysis separates
V-ATPase subunits into expected clades with orthologous sequences. Annotation of the
genome is a critical step towards developing directed pest management strategies to reduce the spread of HLB throughout the citrus industry.
Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of ...higher order chitin structures, such as long fibers and bundles, which contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also be involved in bacterial defense. Here, we report the manual annotation of four CDA genes from the Asian citrus psyllid,
, laying the groundwork for future study of these genes.
The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, ...we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of
the Asian citrus psyllid. This insect is the vector for the bacterial pathogen
Liberibacter asiaticus (
Las), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on
and
identified in the psyllid genome,
likely possesses a circadian model similar to the lepidopteran butterfly,
. Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology.
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also ...pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence ...in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment—(1) Assessing Laboratory Work and Scientific Thinking; (2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; (3) Appraising Forms of Scientific Communication; and (4) Metacognition of Learning—along with a set of practices for each aim. These aims and practices of assessment were then integrated with previously developed models of course-based research instruction to reveal an assessment program in which instructors provide extensive feedback to support productive student engagement in research while grading those aspects of research that are necessary for the student to succeed. Assessment conducted in this way delicately balances the need to facilitate students’ ongoing research with the requirement of a final grade without undercutting the important aims of a CRE education.
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