Biology subjects

Lam, D. K.

Publications and source records attributed to Lam, D. K..

5 recordsLinked to original sources

bioRxiv2025

Omnivorous diets of sympatric duck species in a subtropical East Asia wetland unveiled by multi-marker DNA metabarcoding

The East Asian-Australasian Flyway (EAAF) is experiencing notable population decreases in its migratory waterbird species. Our understanding of the foraging ecology of these waterbird species, including ducks, is crucial for monitoring and safeguarding their food sources and wetland habitats. Here, we used a DNA metabarcoding approach to analyze the fecal DNA from duck species to elucidate their dietary composition during the wintering period in a subtropical East Asian wetland. By employing multiple markers (18S, COI, and trnL) targeting different taxonomic groups and levels, we offered a comprehensive dietary analysis for omnivores that consume both plants and animals. We revealed the dietary compositions of common migratory duck species and their intraspecific and interspecific variations. While ducks are generally known to be omnivorous, Anas crecca had a more specialized diet and was primarily herbivorous throughout winter. In contrast, the sympatric Mareca penelope and Spatula clypeata exhibited a more omnivorous foraging behavior. Moreover, A. crecca displayed less dietary variation among individuals, while individuals of M. penelope and S. clypeata were highly variable in their diets. Comparing our results with those of studies conducted in different regions, we found that the dietary compositions of these duck species varied to different degrees across geographic locations. This variation underscores the flexibility of these duck species in their diets and their adaptable foraging strategies. Our findings also indicate that grasslands rich in herbaceous plants and aquatic environments abundant in small aquatic invertebrates are vital foraging habitats for duck species during their winter stay.

ecology↗

bioRxiv2024

Temporal characterization of the viral load of psittacine beak and feather disease virus in rosy-faced lovebirds (Agapornis roseicollis)

Psittacine beak and feather disease virus (PBFDV) is a widespread and highly pathogenic virus in parrots (Psittaciformes), threatening both captive and wild populations over the world. The disease typically presents with feather and beak abnormalities, along with possible immune system suppression. No cure or commercialized vaccine is currently available. Our understanding of the Psittacine beak and feather disease often come from infected individuals with visible symptoms. Limited knowledge exists regarding the pathology and role of asymptomatic individuals in disease transmission. Asymptomatic individuals could shed virus in their crop secretion, feces, or feathers. In this study, we investigated the temporal change in viral load in feather and fecal samples from 17 asymptomatic rosy-faced lovebirds (Agapornis roseicollis). We developed a qPCR assay for PBFDV viral load quantification in the studied lovebirds. Our results showed that most of the individuals had very low viral load, while three individuals with high viral load at the beginning of the experiment were observed to exhibit a decreasing trend in viral load in both fecal and feather samples. Surprisingly, the viral load in an individual can drop from a high level to an undetectable level within three months, which is contrary to the prevailing notion that the disease is highly lethal with few reports of complete recovery. We also showed that viral load in feathers was higher than in feces. Our study provides valuable insights into the infection dynamics of PBFDV in asymptomatic individuals and contribute to the understanding of disease transmission in parrots.

ecology↗

bioRxiv2022

A search for "perio-probiotics" by longitudinal dissection of oral bacterial community shifts during the onset and resolution of gingivitis

AimTo understand the spatiotemporal dynamics of bacterial succession during gingivitis, and to identify taxa with a critical role in gum health with prognostic value. Materials and methodsLongitudinal microbiome data were collected from 15 individuals after completely discontinuing all forms of oral hygiene, and subsequently reintroducing it for three and two weeks, respectively. Sequences from the 16S rRNA V4-V5 gene region from sub- and supra-gingival plaque, saliva, and tongue sites were annotated and mapped to a reference tree of Human Oral Microbiome Database sequences. ResultsSuspending oral hygiene induced gingivitis, which was resolved after its resumption to baseline. Most significant shifts in bacterial abundance were observed in dental plaque, but not in saliva and tongue sites. During gingivitis-induction, baseline microbiota dominated by Streptococcus, was superseded by increased Prevotella, Fusobacterium, Leptotrichia, and Porphyromonas genera. Converse to its decline during disease-induction, gum health restoration was accompanied by a significant increase in streptococci. ConclusionWe present the most comprehensive, spatiotemporal map of bacterial succession during gingivitis onset and resolution. We have identified taxa with potential as probiotic candidates for gum disease (i.e., perio-probiotics), and suggest tooth-associated plaque and not saliva or tongue plaque should be used in future prognostic tests.

microbiology↗

bioRxiv2020

A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates

FOXA pioneer transcription factors (TFs) displace nucleosomes and prime chromatin across enhancers of different endodermal organs in multipotent precursors before lineage induction. Here, we examined patterns and mechanisms of FOXA target site engagement using human pluripotent stem cell models of endodermal organ development. Unexpectedly, we find that only a subset of pancreatic, hepatic, and alveolar enhancers are FOXA-primed, whereas the majority are unprimed and engage FOXA only upon lineage induction. Analysis of sequence architecture revealed more abundant and stronger FOXA motifs at primed than unprimed enhancers and enrichment for lineage-specific TF motifs at unprimed enhancers. We show that FOXA recruitment to unprimed enhancers specifically depends on lineage-specific TFs, suggesting that regulatory DNA sequence logic governs temporal FOXA recruitment. Our findings suggest that FOXA-mediated enhancer priming broadly facilitates initiation of organ lineage programs, while secondary FOXA recruitment by lineage-specific TFs to the majority of enhancers confers organ specificity to gene expression.

genomics↗

bioRxiv2020

Directed Evolution of Adenine Base Editors with Increased Activity and Therapeutic Application

The foundational adenine base editors (e.g. ABE7.10) enable programmable C*G to T*A point mutations but editing efficiencies can be low at challenging loci in primary human cells. Here we further evolve ABE7.10 using a library of adenosine deaminase variants to create ABE8s. At NGG PAM sites, ABE8s result in [~]1.5x higher editing at protospacer positions A5-A7 and [~]3.2x higher editing at positions A3-A4 and A8-A10 compared with ABE7.10. Non-NGG PAM variants have a [~]4.2-fold overall higher on-target editing efficiency than ABE7.10. In human CD34+ cells, ABE8 can recreate a natural allele at the promoter of the {gamma}-globin genes HBG1 and HBG2, with up to 60% efficiency, causing persistence of fetal hemoglobin. In primary human T cells, ABE8s achieve 98-99% target modification which is maintained when multiplexed across three loci. Delivered as mRNA, ABE8s induce no significant levels of sgRNA-independent off-target adenine deamination in genomic DNA and very low levels of adenine deamination in cellular mRNA.

genomics↗