Article
Entomology
Stephen T. Ferguson, Isaac Bakis, Nicholas D. Edwards, Laurence J. Zwiebel
Summary: Age-related changes in behavior and sensory perception have been observed in various animal species. In ants, workers demonstrate different olfactory responses based on their roles and these responses vary with age. A compound called 3-methylindole elicits stronger responses in minor nurses than in foragers of the same age, indicating its potential importance in brood care.
Article
Behavioral Sciences
Thienthanh Trinh, Renee Ouellette, Charissa de Bekker
Summary: Parasites manipulate host behavior for successful transmission, affecting host circadian clock, olfaction, and communication, ultimately reducing ant foraging activity and effectiveness. Ophiocordyceps-infected ants lose activity rhythm, display decreased foraging abilities, and exhibit weakened communication with nestmates compared to healthy ants.
Article
Biology
S. T. Ferguson, I. Bakis, N. D. Edwards, L. J. Zwiebel
Summary: The study reveals that there are significant differences in olfactory sensitivity and odor coding between minor and major workers in Camponotus floridanus ant colonies. Minors primarily display excitatory responses to olfactory stimuli, while majors manifest suppressed responses. However, both minors and majors show excitatory responses to conspecific cuticular extracts. Moreover, majors exhibit enhanced aggression and killing abilities towards non-nestmate foes. The findings support the hypothesis that minors are multipotential workers and majors are specialized soldiers with specific olfactory sensitivity.
Article
Entomology
Gabriela Perez-Lachaud, Franklin H. H. Rocha, Jean-Paul Lachaud
Summary: We report the occurrence of Horismenus floridensis attacking Camponotus atriceps in southern Mexico, expanding the distribution and potential host range for this eulophid wasp. This is the second host ant ever recorded for H. floridensis and the first reliable record of C. atriceps as a host for this eulophid wasp.
NEOTROPICAL ENTOMOLOGY
(2023)
Article
Cell Biology
Yun Shi, Julia P. Bethea, Hannah L. Hetzel-Ebben, Maicon Landim-Vieira, Ross J. Mayper, Regan L. Williams, Lauren E. Kessler, Amanda M. Ruiz, Kathryn Gargiulo, Jennifer S. M. Rose, Grayson Platt, Jose R. Pinto, Brian K. Washburn, P. Bryant Chase
Summary: The study on the mandibular muscle structure and function of major workers of the Florida carpenter ant revealed features that explain the rightward shift of calcium activation and structural implications for the troponin complex. This sheds light on how mandibular muscle fibers perform various functions and the role of troponin in these tasks.
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY
(2021)
Article
Entomology
Mark E. Mankowski, Jeffrey J. Morrell, Patricia K. Lebow
Summary: The yeast Schwanniomyces polymorphus is associated with the infrabuccal pocket in the carpenter ant Camponotus vicinus, and may play a supplemental role in ant nutrition and development, particularly when ants are fed nutrient-deficient diets. The potential effects of this yeast on brood development were examined over a 12 week period, showing that the yeast may help ants to more efficiently assimilate nutrients, especially in diets deficient in sterols. The heat/chemical defaunation process significantly affected brood development, but non-defaunated ant groups fed a diet lacking both B vitamins and cholesterol and exposed to live S. polymorphus resulted in higher brood weights and number of worker ants produced.
Article
Microbiology
Yuliya Zakalyukina, Ilya A. Osterman, Jacqueline Wolf, Meina Neumann-Schaal, Imen Nouioui, Mikhail Biryukov
Summary: In this study, a novel actinobacterial strain A23(T) was isolated from adult ant Camponotus vagus collected in the Ryazan region, Russia. Phylogenetic analyses showed that strain A23(T) is closely related to Amycolatopsis pretoriensis DSM 44654(T). Based on the phenotypic, genomic, and phylogenetic data, strain A23(T) represents a new species, Amycolatopsis camponoti sp. nov.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Behavioral Sciences
Patrizia D'Ettorre, Patricia Meunier, Pietro Simonelli, Josep Call
Summary: Carpenter ants are able to make efficient decisions based on both relative quantity and relative position, discriminating between different sizes of brood piles and learning to identify a landmark associated with food. This highlights their ability to use quantitative information in natural contexts, with potential implications for their ecological success.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Christopher Faulk
Summary: In this study, the researcher successfully assembled the genome of the black carpenter ant using nanopore sequencing technology at a lower cost and time. The quality of the assembly was accurately assessed. The study also included the assembly of the mitochondrial genome and symbiotic bacteria genomes, as well as measurements of DNA methylation and hydroxymethylation. This method enables low-resource labs to obtain high-quality genome assemblies at a lower cost.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Andrew Z. Dong, Nural Cokcetin, Dee A. Carter, Kenya E. Fernandes
Summary: This study investigates the antimicrobial activity and chemical properties of honey produced by the Australian honeypot ant. Results show that the honeypot ant honey has strong activity against Staphylococcus aureus but not other bacteria, and strong non-peroxide activity against Cryptococcus and Aspergillus sp. The antimicrobial activity and chemical properties of honeypot ant honey differ significantly from jarrah and manuka honey produced by honey bees. The bacterial microbiome of honeypot ants is dominated by Candidatus Blochmannia, while the fungal microbiome is dominated by the plant-associated genus Neocelosporium.
Article
Multidisciplinary Sciences
Ian Will, William C. Beckerson, Charissa de Bekker
Summary: Parasitic fungi manipulate host behavior through protein-protein interactions, and machine learning predictions provide new hypotheses on the mechanisms underlying this behavioral manipulation. This study predicted host-parasite protein-protein interactions and identified several key proteins involved in the manipulation of zombie ant behavior.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Hong-Dong Li, Changhuo Yang, Zhimin Zhang, Mengyun Yang, Fang-Xiang Wu, Gilbert S. Omenn, Jianxin Wang
Summary: IsoResolve is a novel approach for isoform function prediction that leverages gene function prediction models with domain adaptation to improve performance. It treats gene-level and isoform-level features as source and target domains respectively, and uses domain adaptation to project them into a latent variable space for more accurate predictions.
Article
Plant Sciences
Dianella Iglesias, Marcos de Donato Capote, Alfonso Mendez Tenorio, Ana Victoria Valdivia, Claudia Gutierrez-Garcia, Sujay Paul, Hafiz M. N. Iqbal, Maria Luisa Villarreal, Ashutosh Sharma
Summary: In this study, a comparative transcriptome analysis was conducted to identify candidate genes involved in the galphimine synthesis pathway, using two contrasting populations of Galphimia spp. The results provide insights into the molecular mechanisms underlying galphimine production in Galphimia plants.
Article
Biology
Roberto Vera Alvarez, Leonardo Marino-Ramirez, David Landsman
Summary: The researchers compared multiple BLAST sequence alignments using AWS and GCP and found that public cloud providers are a practical and cost-effective alternative for conducting advanced computational biology experiments. Their study aimed to establish an estimate of the cost and compute time needed for the execution of multiple BLAST runs in a cloud environment.
Article
Environmental Sciences
Lan Zhang, Nicholas W. Johnson, Yun Liu, Yu Miao, Ruihuan Chen, Hong Chen, Qian Jiang, Zhongpei Li, Yuanhua Dong, Shaily Mahendra
Summary: This study demonstrated that a Phanerochaete chrysosporium fungal-luffa fiber system efficiently degrades sulfonamide antibiotics in cow urine wastewater. Transcriptomic, metabolomic, and free radical analyses were conducted to uncover the molecular mechanisms involved in the degradation of SDM and SDZ. The results suggest that carbohydrate-active enzymes and oxidoreductases play crucial roles in the degradation process. EPR spectroscopy revealed the generation of free radicals during the biodegradation, indicating a potential free radical pathway for the transformation of SDM and SDZ.
Article
Ecology
Simon A. B. Riedl, Matthias Voelkl, Anja Holzinger, Julia Jasinski, Valerie Jerome, Thomas Scheibel, Heike Feldhaar, Ruth Freitag
Summary: The intestinal cells of the earthworm Eisenia fetida are suitable for studying the toxic effects of environmental pollutants on a cellular level. Exposure to pollutants and soil elutriates led to a decrease in metabolic activity of the cells. Additionally, microplastic particles did not show active uptake, but had dose and size dependent effects on metabolism that may correlate with organismic effects.
Article
Neurosciences
Franziska Karl-Schoeller, Meik Kunz, Luisa Kress, Melissa Held, Nadine Egenolf, Anna Wiesner, Thomas Dandekar, Claudia Sommer, Nurcan Ueceyler
Summary: Neuropathic pain is common in peripheral neuropathy patients, and the study investigated the role of miR-21 in this pain. Inhibition of miR-21-5p reversed mechanical and heat hypersensitivity in mice with nerve injury, leading to a decrease in pro-inflammatory mediators. The study also found different expression patterns of miR-21-5p and pro-inflammatory mediators in human patients with neuropathic pain syndromes.
EXPERIMENTAL NEUROLOGY
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Frank Eisenhaber, Juilee Thakar, Alicia Ponte-Sucre, Thomas Dandekar
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Stefan Loroch, Dominik Kopczynski, Adriana C. Schneider, Cornelia Schumbrutzki, Ingo Feldmann, Eleftherios Panagiotidis, Yvonne Reinders, Roman Sakson, Fiorella A. Solari, Alicia Vening, Frauke Swieringa, Johan W. M. Heemskerk, Maria Grandoch, Thomas Dandekar, Albert Sickmann
Summary: This study introduces a novel strategy for positive-pressure 96-well filter-aided sample preparation (PF96), which significantly increases throughput and demonstrates high reproducibility. The study confirms the excellent reproducibility and stability of PF96 at the protein level, as well as its compatibility with nanoLC-MS instrumentation. This method has promising applications in biomedical and clinical research.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Juan Pablo Prada, Luca Estelle Maag, Laura Siegmund, Elena Bencurova, Liang Chunguang, Eleni Koutsilieri, Thomas Dandekar, Carsten Scheller
Summary: This study proposes using excess mortality data to determine the basic reproduction number (R0) of SARS-CoV-2, regardless of RT-PCR testing capacity. The uncorrected R0 values based on incidence data were 2.56 (cases) and 2.03 (deaths), but after correcting for increased testing, the R0 values were 1.86 (cases) and 1.47 (deaths). The R0 value based on excess deaths was calculated to be 1.34. The study suggests that R0 is much lower than previously thought and aligns with the observed seasonal pattern of COVID-19 infections in Europe.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, General & Internal
Shishir K. Gupta, Oezge Osmanoglu, Rashmi Minocha, Sourish Reddy Bandi, Elena Bencurova, Mugdha Srivastava, Thomas Dandekar
Summary: This study successfully identified novel epitopes for vaccine design against C. auris using evolutionary information and reverse vaccinology approach. Two effective T-cell epitopes were found to have potential for the treatment of C. auris infection. In vivo experiments are needed to further test the efficacy of the designed vaccine.
FRONTIERS IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Aylin Caliskan, Samantha A. W. Crouch, Sara Giddins, Thomas Dandekar, Seema Dangwal
Summary: In this study, the researchers analyzed a publicly available RNA-Seq dataset to investigate differentially expressed genes related to progeria and aging. They identified several genes involved in both natural aging and progeria, indicating their potential roles in the aging process and highlighting the need for further research.
Article
Biochemistry & Molecular Biology
Edita Sarukhanyan, Thomas Dandekar
Summary: Microtubules are essential for maintaining cell shape and Tau protein plays a role in regulating their plasticity. Abnormal phosphorylation of Tau proteins leads to the formation of neurofibrillary tangles, which are linked to Alzheimer's disease. In this study, a potential drug candidate, compound 23, was designed using computer simulations to target the phosphorylated Tau-microtubule complexes. The results showed that compound 23 can bind to and stabilize phosphorylated Tau proteins on the surface of microtubules, preventing their aggregation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Review
Biochemistry & Molecular Biology
Elena Bencurova, Aman Akash, Renwick C. J. Dobson, Thomas Dandekar
Summary: In this article, the fundamental aspects of DNA storage and recent advances in this field are discussed, with a focus on natural processes and solutions that can be utilized. New methods for efficient DNA and nucleotide storage inspired by nature are highlighted. Within a few years, DNA-based information storage may become a complement to current electronic data storage systems. Various aspects, such as rapid and directed access, regulatory signals and modulation, and integrated high-density storage and processing modules, are examined. DNA storage has practical applications in biotechnology and human genetics. The potential of DNA storage in synthetic biology and its advantages in direct storage operations are also explored. The use of biology concepts from chromosomal storage, nucleic acid processing, and polymer material sciences will lead to new applications gradually replacing classical information storage methods over time (decades).
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Chao Han, Pengxuan Ren, Medina Mamtimin, Linus Kruk, Edita Sarukhanyan, Chenyu Li, Hans-Joachim Anders, Thomas Dandekar, Irena Krueger, Margitta Elvers, Silvia Goebel, Kristin Adler, Goetz Muench, Thomas Gudermann, Attila Braun, Elmina Mammadova-Bach
Summary: This study analyzed the collagen- and CRP-binding surfaces of GPVI monomers and dimers using computational modeling and bioinformatics, and compared them with other mammalian GPVI isoforms. Experimental results show that the EA-20 antibody inhibits platelet adhesion and aggregation in response to collagen and CRP, but not to fibrin, and prevents thrombus formation in whole blood. Therefore, the blockade of this minimal collagen-binding epitope of GPVI with the EA-20 antibody could represent a new anti-thrombotic approach.
Article
Biochemistry & Molecular Biology
Kunkun Li, Juan Prada, Thomas Dandekar, Daniel S. C. Damineli, Kai R. R. Konrad
Summary: The polar growth and guidance of pollen tubes are regulated by chemical and electrical signaling cues. The functional relationship between membrane voltage (V-m), Ca2+, and H+ dynamics in pollen tubes is largely unclear. In this study, live-cell imaging and cross-correlation analysis revealed distinct relationships between these signals along pollen tubes, with Ca2+ and H+ correlating with V-m dynamics at the tip, while only H+ correlated with V-m at the shank. These findings suggest spatially confined chemo-electric coupling supports the propagation of voltage and pH waves along non-growing pollen tubes, preceded by short-lasting but high amplitude tip Ca2+ spikes.
Article
Multidisciplinary Sciences
Joerg Mueller, Oliver Mitesser, H. Martin Schaefer, Sebastian Seibold, Annika Busse, Peter Kriegel, Dominik Rabl, Rudy Gelis, Alejandro Arteaga, Juan Freile, Gabriel Augusto Leite, Tomaz Nascimento de Melo, John G. Lebien, Marconi Campos-Cerqueira, Nico Bluethgen, Constance J. Tremlett, Dennis Boettger, Heike Feldhaar, Nina Grella, Ana Falconi-Lopez, David A. Donoso, Jerome Moriniere, Zuzana Burivalova
Summary: This study used bioacoustics and metabarcoding to measure forest recovery post-agriculture in a global biodiversity hotspot in Ecuador. The results showed that the composition of vocalizing vertebrates identified by experts reflected the restoration gradient, and two automated measures correlated well with restoration. Furthermore, both measures also reflected the composition of non-vocalizing nocturnal insects. This study demonstrates the effectiveness of new technologies in monitoring forest recovery.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Aylin Caliskan, Deniz Caliskan, Lauritz Rasbach, Weimeng Yu, Thomas Dandekar, Tim Breitenbach
Summary: Machine learning techniques are widely used to analyze single-cell expression data, impacting various fields such as cell annotation, clustering, and signature identification. This framework evaluates gene selection sets based on their ability to effectively separate defined phenotypes or cell groups. It overcomes the limitation of identifying a small gene set with high information content for phenotype separation, and provides corresponding code scripts. The selected subset of genes facilitates human interpretability of phenotype differences, and can potentially explain the causal relationships between genes and phenotypes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Rana Salihoglu, Mugdha Srivastava, Chunguang Liang, Klaus Schilling, Aladar Szalay, Elena Bencurova, Thomas Dandekar
Summary: PRO-Simat is a simulation tool that analyzes protein interaction networks, their dynamic changes, and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualization using a database of over 8 million protein-protein interactions across 32 organisms. The tool also allows for dynamical network simulation using the Jimena framework, offering in-depth analysis of protein interactions. It has demonstrated applications in understanding differentiation pathways, oncolytic virus development, and optogenetic control of nucleotide processing protein networks. PRO-Simat can be accessed at https://prosimat.heinzelab.de/ as a web-based query server.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Aylin Caliskan, Seema Dangwal, Thomas Dandekar
Summary: In the rapidly evolving field of biomedical research, the emergence of big data has provided researchers with opportunities to explore biological complexities. However, to ensure the reliability and reproducibility of data-driven findings, it is crucial to have detailed and accurate metadata.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
